|
|
| Entry A:27, R:58, T:ENTRY, I:20600
| Information about a single entry deposited. This does not correcpond directly to the actual macromolecule because the symmetry has not been applied yet |
| Assembly A:21, R:29, T:ASSEMBLY, I:28300
| An assembly represents the actual macromolecule, the complete collection of associated macromolecules and associated small molecules - including solvent. This represents a level higher than tertiary structure, since these are the main components of the assembly can exist on their own. An example of this would be an antibody bound to lysozyme. There is at least one assembly per experimental observation.
The whole organisation of the structural and other parts of the database is based on assemblies. We consider the assembly as the primary biologically sensible 3D structure, and we do not try to concentrate in the original non-symmetric unit of the PDB file.
This means that every chain and its residues and atoms are copied and transformed together with their coordinates, for every occurance of a single chain in an assembly and for all assemblies.
For example if an entry 1xxx could be assemblied in two ways and each assembly includesthe non-symmetric chain A 4 times, then chain A will be copied and transformed 8 times.
One of these copies is marked with the non-assembly-valid flag, and in this way the original non-symmetric PDB structure may be extracted.
In rare cases where there are entities (waters or ligands), that cannot be associated with an assembly, then a fake assembly is created to provide a placeholder. |
| Chain A:46, R:33, T:CHAIN, I:194000
| Molecule entities in an assembly. It includes Data items such as (chemical composition, name, and source) about the molecules that are present in the crystallographic structure. Chains entities are of three types: polymer, non-polymer and water. Note that the water category includes only water, ordered solvent such as sulfate ion or acetone would be described as individual non-polymer entities. This entity also describe the chemistry of the molecules under investigation, and can most usefully be thought of as the ideal groups to which the structure is restrained or constrained during refinement and also how these molecules constitute the biological unit and the symetry operators (REMARK 300 and 350) that need to be applied to the coordinates in order to expand these molecules. |
| Model A:6, R:20, T:MODEL, I:59500
| In several cases (usually NMR experiments) different alternative sets of coordinates have been found for a single molecule. These are represented by different models |
| Molecule A:16, R:15, T:MOLECULE, I:92500
| The biological entity of a macromolecule chain, defined by its residue sequence. Several chains of an entry may be different configurations in the 3D space, of the same molecule.
Molecules can be of 2 types
a) Normal PDB molecules (sequences) that are directly associated with a chain structure.
b) Molecule (sequence) fragments. These are parts of a parent PDB molecule that are referred
by another entity or database (like Swiss-prot etc), but they refer to the actual chain structure
through their parent molecule.
In addition there are also entities defined for non-polymers and water-groups
|
| Chain Sequence A:7, R:3, T:CHAIN_ALL_SEQ, I:0
| The protein sequence of a chain that includes even unobserved residues (without structural coordinate data) |
| Observed Sequence A:7, R:3, T:CHAIN_OBS_SEQ, I:0
| The protein sequence of a chain that includes only observed residues (with structural coordinate data) |
| Assembly per Model A:23, R:3, T:ASSEMBLY_MODEL, I:23500
| This includes some partial information about the properties of an assembly per model. It is not complete, in the sense that it does not include that for each model and for each assembly, but is incorporated in order to justify the formation of assemblies. |
| Atom A:26, R:4, T:ATOM, I:78000000
| Abstraction of a macromolecule atom where its actual configuration (coordinates etc) is not considered. Alternative coordinates due to ALT codes, assemblies or assembly symmetry transformations, refer to the same abstract atom. |
| Atom Data A:42, R:12, T:ATOM_DATA, I:154000000
| The actual atom (the PDB atom line). The application of the assembly symmetry transformations, have also instanciated atoms for all actual chains of all assemblies of an entry. |
| Matrix A:17, R:4, T:MATRIX, I:162000
| Transformation matrix that has been used for the generation of an assembly chain |
| Alt A:7, R:4, T:ALT, I:5520
| An abstraction of an alternative location of an atom. This corresponds to an ALT code in a PDB entry. |
| Sequence Alignment A:29, R:6, T:CHAIN_SEQ_ALIGNMENT, I:2740000
| Chains that their protein sequences can be satisfactory aligned, based on some predefined limits.
The sequence alignment is calculated based on the FASTA algorithm (http://fasta.bioch.virginia.edu/fasta/cgi/searchx.cgi?pgm=fa) |
| Structural Alignment A:43, R:6, T:CHAIN_STR_ALIGNMENT, I:25800000
| Chains that their structure can be satisfactory aligned in 3D space, based on some predefined limits.
The structure is calculated based on SSM (http://www.ebi.ac.uk/msd-srv/ssm/) |
| Residue A:26, R:22, T:RESIDUE, I:19200000
| The component that an entity contains. For example this can be the residue of a polymer chain. But it can also be a molecule of a non-polymer or water entity |
|
Reference attributes:Entry Id - Naming attributes:Accession Code |
C:ENTRY_ID, S:10, A:4.0 | The database identifier of the Entry |
C:ACCESSION_CODE, S:8, A:4.0 | The PDB accession code of the entry |
Class 1  C:CLASS_1, S:10, A:3.0 | |
Class 2 C:CLASS_2, S:10, A:1.0 | |
Class 3 C:CLASS_3, S:10, A:1.0 | |
Creation Date  C:CREATION_DATE, S:0, A:7.0 | |
NDB crystal grow details  C:DETAILS_NDB, S:2000, A:1.0 | Text description of crystal grow procedure. Examples PEG 4000, potassium phosphate, magnesium chloride, cacodylate |
Entry Version  C:ENTRY_VERSION, S:10, A:1.0 | |
Experiment Type C:EXPERIMENT_TYPE, S:255, A:27.0 | |
Header C:HEADER, S:80, A:17.0 | |
Header 1 C:HEADER_1, S:10, A:1.0 | |
Header 2 C:HEADER_2, S:10, A:1.0 | |
Header 3 C:HEADER_3, S:10, A:1.0 | |
Model Details C:MODEL_DETAILS, S:240, A:1.0 | |
PDB Experiment Type C:PDB_EXPERIMENT_TYPE, S:255, A:1.0 | The experiment type as described in the PDB specification |
Processed By C:PROCESSED_BY, S:8, A:4.0 | The organisation or centre that the macromolecular structure was deposited, for example: BNL,EBI,PDBJ,RCSB,NDB,PRAGUE |
Processing Status C:PROCESSING_STATUS, S:25, A:7.0 | |
Rcn Id  C:RCN_ID, S:10, A:3.0 | The database identifier of the Rcn |
Release Status C:REL_STATUS, S:1, A:1.0 | A flag that specifies if the current entry is publicly released or not |
Release Date C:RELEASE_DATE, S:0, A:7.0 | |
Resolution  C:RES_VAL, S:0, A:3.0 | Contains the effective resolution of the refinement. This information may come from a number of sources. |
Ret1Id C:RET1_ID, S:10, A:2.0 | The database identifier of the Ret1 |
Rsf Id C:RSF_ID, S:10, A:1.0 | The database identifier of the Rsf |
Experiment type C:SHORT_EXPERIMENT_TYPE, S:255, A:4.0 | The experimental technique used (XRAY,NMR) |
Resolution Source C:SOURCE, S:10, A:5.0 | The source of the effective resolution. It may take the values
1)AUTH:Author supplied
2)PDBR2:Taken from REMARK 2 of a PDB file
3)SFCHECK:Calculated by SFCHECK using deposited structure factors
|
Title C:TITLE, S:2000, A:70.0 | The TITLE record contains a title for the experiment or analysis that is represented in the entry. It should identify an entry in the PDB in the same way that a title identifies a paper. * The title of the entry is free text and should describe the contents of the entry and any procedures or conditions that distinguish this entry from similar entries. It presents an opportunity for the depositor to emphasize the underlying purpose of this particular experiment. Some items that may be included in TITLE are: Experiment type, Description of the mutation. The fact that only alpha carbon coordinates have been provided in the entry. |
Version C:VERSION, S:0, A:1.0 | |
has    | |
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referred | |
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has | The entry where the authors are in citations |
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has | Reverse relation: of of Reverse entity: Alt - Relation attributes: Entry Id |
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has | The keywords of the entry |
has | |
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has | |
has | The xray-data of the entry |
has | Reverse relation: of of Reverse entity: Turn - Relation attributes: Entry Id |
has | |
has | |
has | Reverse relation: of of Reverse entity: Site - Relation attributes: Entry Id |
has | |
has | |
has | |
has | |
has | |
has | The authors of the entry |
has | Reverse relation: of of Reverse entity: Atom - Relation attributes: Entry Id |
has | |
has | |
has | |
has | |
has | |
has  | The xray-data of the entry |
has | |
has | |
aligned | |
|
Reference attributes:Assembly Id - Naming attributes:Accession Code,Assembly Serial |
C:ASSEMBLY_ID, S:10, A:4.0 | The database identifier of the Assembly |
C:ACCESSION_CODE, S:8, A:4.0 | The PDB accession code of the entry |
C:ASSEMBLY_SERIAL, S:38, A:2.0 | The serial identifier of the assembly in the entry |
Assembly Class C:ASSEMBLY_CLASS, S:2, A:2.0 | Label providing if this is a homodimer (HO) or a heterodimer (HE) |
Assembly Form C:ASSEMBLY_FORM, S:50, A:4.0 | A string of the chains in the assembly and their number of occurences forming a chain formula of the type, A2B1 for example for a hetero-trimeric complex containing two chemically distinct chains. or A3B3C3 for example for a hetero-trimeric complex containing three chemically distinct chains. |
Assembly Title C:ASSEMBLY_TITLE, S:255, A:3.0 | A title that denotes special properties of the assembly. For example 'Fake Assembly' for the single assembly in these entries where there are entities (chains, waters or ligands) that are not included in any other real assembly. In such cases a fake assembly is constructed for data organisation purposes (of course it is not biologically sensible) to provide a placeholder for these remaining entities |
Assembly Type C:ASSEMBLY_TYPE, S:50, A:8.0 | The type of the tertiary symmetry (MONOMERIC,DIMERIC,TETRAMERIC ...) of the assembly |
Entry Id C:ENTRY_ID, S:10, A:4.0 | The database identifier of the Entry |
Number of chains C:NUM_CHAINS, S:8, A:2.0 | The number of chains in the assembly |
Number non-standard Atoms C:NUM_NSTD_ATOM, S:8, A:2.0 | The total number of non-standard hetero atoms (HETATM) in the assembly |
Number of Residues C:NUM_RESIDUES, S:8, A:3.0 | The total number of residues in the assembly |
Number of Di-Sulphides C:NUM_XCHAIN_SS, S:8, A:2.0 | Inter-Chain Di-sulphides to be used in the analysis of likely generated quaternary structures based on the methods of Kossiakoff, Dijkstra and Jane Richardson |
Release Status C:REL_STATUS, S:1, A:1.0 | A flag that specifies if the current entry is publicly released or not |
Score C:SCORE, S:8, A:2.0 | This factor describes how well the chains of the assembly match and are densly packed in space. It can have negative values and smaller (more negative) values mean better matching of chains. For example score < -10 will give back the most perfectly packed assemblies |
N Repeat C:N_REPEAT, S:4, A:1.0 | |
Status C:STATUS, S:10, A:3.0 | A label that provides the status of the assembly (OK,XPACK) |
Repeat Dist C:REPEAT_DIST, S:0, A:1.0 | |
N Unique C:N_UNIQUE, S:4, A:1.0 | |
Helical Height C:HELICAL_HEIGHT, S:0, A:1.0 | |
Helical Twist C:HELICAL_TWIST, S:0, A:1.0 | |
Search Assembly Type C:SRCH_ASSEMBLY_TYPE, S:50, A:0.0 | The assembly textual description of types (in a comma seperated list) that match with the type of this assembly. For example for a dimeric assemlby this attribute has the value:'DIMERIC,MULTIMERIC' |
has | |
has | |
has | The active site angle to planes that are in the assembly |
has | The active site angles that are in the assembly |
has | |
has | |
has | The atom coordinates of the assembly |
has | The active site contains of the assembly |
has | The sheets of the assembly |
has | The secondary summary of the assembly |
has | The secondary residue data of the assembly |
has | The residues of the assembly |
has | The active site planes of the assembly |
has | The motifs of the assembly |
has | The helix interactions of the assembly |
has | The helices of the assembly |
has | The hairpins of the assembly |
has | |
has | |
has | The chains of the assembly |
has | The assembly models |
of    | The entry of the assembly |
has | The turns of the assembly |
has | The swiss-prot mappings of the assembly |
has | The strands of the assembly |
has | The sheet orders of the assembly |
has | The hydrogen bonds of the assembly |
has | The bulges of the assembly |
|
Reference attributes:Chain Id - Naming attributes:Accession Code,Assembly Serial,Chain Code |
C:CHAIN_ID, S:10, A:5.0 | The database identifier of the Chain |
C:ACCESSION_CODE, S:8, A:4.0 | The PDB accession code of the entry |
C:ASSEMBLY_SERIAL, S:38, A:2.0 | The serial identifier of the assembly in the entry |
C:CHAIN_CODE, S:8, A:3.0 | The standard code of the chain that uniquely identifies it in the assembly. It is an extension of the PDB chain Id.
In cases where symmetry operations have been applied to a chain, these chains are named with a numeric suffix, ie. A,A1,A2,A3 ...
The chain id specified in the PDB file is also ignored for waters and bound molecules, and their codes are derived from the name of the chain that they are bound to.
Finally there are no "null" chain codes and in cases where no id was specified in the PDB file, then arbitrary chain codes are assigned (i.e. A,B) |
Accessible Surface Area C:ASA, S:0, A:2.0 | Accessible surface area of the chain in the assembly |
Assembly Class C:ASSEMBLY_CLASS, S:2, A:2.0 | Label providing if this is a homodimer (HO) or a heterodimer (HE) |
Assembly Form C:ASSEMBLY_FORM, S:50, A:5.0 | A string of the chains in the chain's assembly and their number of occurences forming a chain formula of the type, A2B1 for example for a hetero-trimeric complex containing two chemically distinct chains. or A3B3C3 for example for a hetero-trimeric complex containing three chemically distinct chains. |
Assembly Id C:ASSEMBLY_ID, S:10, A:4.0 | The database identifier of the Assembly |
Assembly Type C:ASSEMBLY_TYPE, S:50, A:9.0 | The type of the tertiary symmetry (MONOMERIC,DIMERIC,TETRAMERIC ...) of the chain's assembly |
Associated Chain Code C:ASSOCIATED_CHAIN_CODE, S:8, A:2.0 | The standard code of the Associated Chain |
Associated Chain Id C:ASSOCIATED_CHAIN_ID, S:10, A:4.0 | The database identifier of the Associated Chain |
Author Code C:AUTH_CODE, S:8, A:1.0 | The original code of the chain as assigned by the author assigned code |
PDB Export Chain Code C:CHAIN_CODE_1_LETTER, S:1, A:1.0 | This is an additional 1 letter code that uniquely identifies it in the assembly. It is arbitrary and its purpose is to be able to export files in PDB format |
PDB Export Residue Increment C:CHAIN_INCR_1_LETTER, S:0, A:2.0 | There are a few cases where there are more chains that the 1 letter code may uniquely identify (more than 52). In these cases, the same 1 letter is reused, but an increment is added to the PDB sequence of their residues (i.e. A with residues 1..100 and chain A with increment 10000 and residues 10000..10100 |
Chain Type C:CHAIN_TYPE, S:1, A:1.0 | The type of the chain (polymer C,non-polymer B,water W) |
Chem Comp Id C:CHEM_COMP_ID, S:10, A:2.0 | The database identifier of the Chem Comp |
Details C:DETAILS, S:2000, A:1.0 | A description of special aspects of the chain entity. |
Chain Accessible Surface Area C:DGAC_ASA, S:0, A:1.0 | Accessible surface area of the chain in the assembly |
Chain Solvation Energy C:DGAC_SOLE, S:0, A:1.0 | Solvation energy of the chain |
Entry Id C:ENTRY_ID, S:10, A:4.0 | The database identifier of the Entry |
Formula Weight C:FORMULA_WGHT, S:0, A:1.0 | Formula mass in daltons of the molecule |
Fragment C:FRAGMENT_FLAG, S:255, A:3.0 | A string to indicate that the chain entity is fragment |
Matrix Id C:MATRIX_ID, S:0, A:4.0 | The database identifier of the Matrix |
Molecule Code C:MOLECULE_CODE, S:255, A:2.0 | Uniquely identifies a molecule in an entry. It does not need be a number; it can be any unique identifier.
|
Molecule Details C:MOLECULE_DETAILS, S:2000, A:8.0 | Description of special aspects of the compounds such as their synonyms.
|
Molecule Engineered C:MOLECULE_ENGINEERED, S:255, A:2.0 | A string to indicate that the chain entity is engineered |
Molecule Id C:MOLECULE_ID, S:10, A:4.0 | The database identifier of the Molecule |
Molecule Name C:MOLECULE_NAME, S:255, A:21.0 | Optionally provides naming information about the molecule |
Chain Msd Code C:MSD_CODE, S:8, A:5.0 | An internal longer code for a chain (defined by MSD) that includes the type of the chain (protein, bound molecule etc). It does not identify uniquely a chain in an assembly; the chain code has to be used instead |
Mutation flag C:MUTATION_STRING, S:40, A:1.0 | A string to indicate that the chain entity is mutation |
Ncbi Tax Id C:NCBI_TAX_ID, S:15, A:1.0 | The NCBI taxonomy identifier (taxid) that points to a node of the taxonomy tree |
Next Id C:NEXT_ID, S:10, A:1.0 | (obsolete) this is not valid for chains |
Valid In Assymetric Unit C:NON_ASSEMBLY_VALID, S:1, A:1.0 | This item is to be used not only in an assembly context, but also to represent the original asymmetric unit |
Number of Residues C:NUM_RESIDUES, S:8, A:2.0 | The number of residues in the chain |
Parent Molecule Id C:PARENT_MOLECULE_ID, S:10, A:1.0 | The database identifier of the Parent Molecule |
PDB Code C:PDB_CODE, S:1, A:1.0 | The original code of the chain as was found in the PDB file |
RCSB Code C:RCSB_CODE, S:8, A:5.0 | An internal longer code for a chain (defined by RCSBD) that includes the type of the chain (protein, bound molecule etc). It does not identify uniquely a chain in an assembly; the chain code has to be used instead |
Spacegroup operator C:RSE_SERIAL, S:0, A:2.0 | The number of the operator within the spacegroup, in standard (International Tables) order, in the list of symmetry equivalent positions for the space group, that was used for this chain |
Solvation energy C:SOLE, S:0, A:2.0 | Solvation energy of the chain |
Serial of chain for molecule C:CHAINMOL_SERIAL, S:0, A:0.0 | This is the serial of the chain for a molecule (sequence). It may be generally expected that structures of the same sequence (molecule) are often quite similar. So in order to use a single representative structure for a sequence one may use only the chains where this attribute equals to "1" (representative structures) |
Symm Asym Id C:SYMM_ASYM_ID, S:8, A:3.0 | The symm_asym identifier |
Synthetic Flag C:SYNTHETIC_FLAG, S:1, A:1.0 | A flag to indicate that the chain entity is synthetic |
Fractional Translation A C:TRANS_A, S:0, A:2.0 | Component of the fractional translation vector applied to this chain (includes both lattice translations and the translational component of the symmetry operator |
Fractional Translation B C:TRANS_B, S:0, A:2.0 | Component of the fractional translation vector applied to this chain (includes both lattice translations and the translational component of the symmetry operator |
Fractional Translation C C:TRANS_C, S:0, A:2.0 | Component of the fractional translation vector applied to this chain (includes both lattice translations and the translational component of the symmetry operator |
Virus Matrix Number C:VIRUS_MATRIX_NUMBER, S:2, A:1.0 | Serial number of matrix operation, within a virus particle |
has | |
aligned | |
aligned | |
has | |
parent | |
has | |
of | The molecule (sequence) that the chain corresponds |
of | The assembly of the chain |
of | The entry of the chain |
has | |
has | |
has | |
has | Reverse relation: of of Reverse entity: Turn - Relation attributes: Chain Id |
has | |
has | |
has | Reverse relation: of of Reverse entity: Site - Relation attributes: Chain Id |
has | |
has | |
has | |
has | |
has | |
of | The matrix used for caclulating the coordinates of the assembly chain |
refers | The ligand that this bound molecule chain refers |
has | |
has | |
of organism | |
has | |
has | |
has | |
has | |
has | |
has | |
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Reference attributes:Model Id - Naming attributes:Accession Code,Model Serial |
C:MODEL_ID, S:10, A:4.0 | The database identifier of the Model |
C:ACCESSION_CODE, S:8, A:4.0 | The PDB accession code of the entry |
Entry Id C:ENTRY_ID, S:10, A:4.0 | The database identifier of the Entry |
C:MODEL_SERIAL, S:3, A:2.0 | The serial identifier of the model in the entry |
PDB Model Serial C:PDB_MODEL_SERIAL, S:3, A:2.0 | The serial of the model as was given in the PDB. Model serial is a more consistent way to identify models since in PDB these serials do not always start from 1 and sometimes get negative numbers.
So there is no simple way to get the first model of an entry. With model serial, this is always the model with serial 0. |
Release Status C:REL_STATUS, S:1, A:1.0 | A flag that specifies if the current entry is publicly released or not |
has | |
has | |
has | |
has | |
has | Reverse relation: of of Reverse entity: Alt - Relation attributes: Model Id |
of | |
has | Reverse relation: of of Reverse entity: Turn - Relation attributes: Model Id |
has | |
has | |
has | |
has | |
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Reference attributes:Molecule Id - Naming attributes:Accession Code,Molecule Code |
C:MOLECULE_ID, S:10, A:4.0 | The database identifier of the Molecule |
C:ACCESSION_CODE, S:8, A:4.0 | The PDB accession code of the entry |
C:MOLECULE_CODE, S:255, A:2.0 | Uniquely identifies a molecule in an entry. It does not need be a number; it can be any unique identifier.
|
Chem Comp Id C:CHEM_COMP_ID, S:10, A:1.0 | The database identifier of the Chem Comp |
Details C:DETAILS, S:2000, A:6.0 | A description of special aspects of the entity |
Entry Id C:ENTRY_ID, S:10, A:4.0 | The database identifier of the Entry |
Formula Weight C:FORMULA_WGHT, S:0, A:1.0 | Formula mass in daltons of the molecule |
Fragment Flag C:FRAGMENT_FLAG, S:255, A:5.0 | |
Molecule Engineered C:MOLECULE_ENGINEERED, S:1, A:1.0 | |
Molecule Name C:MOLECULE_NAME, S:255, A:25.0 | Optionally provides naming information about the molecule |
Mutation String C:MUTATION_STRING, S:40, A:1.0 | Details about an entity mutation. |
Ncbi Tax Id C:NCBI_TAX_ID, S:15, A:1.0 | The NCBI taxonomy identifier (taxid) that points to a node of the taxonomy tree |
Next Id C:NEXT_ID, S:10, A:1.0 | The database identifier of the next molecule segment. This attribute is set for molecule (sequence) fragments only. |
Parent Molecule Id C:PARENT_MOLECULE_ID, S:10, A:2.0 | The database identifier of the Parent Molecule. This attribute is set for molecule (sequence) fragments only, and refers to the complete PDB molecule (sequence) that is instanciated by a chain |
Synthetic C:SYNTHETIC, S:1, A:1.0 | |
Molecule Type C:TYPE, S:10, A:4.0 | Molecule type:
P: Polymer molecule
S: Polymer segment
M: Non-polymer
W: Water group |
parent | |
has | |
has | |
parent | The parent molecule. This relationship is valid for molecule segments than PDB molecules and refers to the actual PDB molecule that is associated with a chain |
of | The actual chains with coordinates that implement this molecule (sequence) |
of | The entry of the molecule |
corresponds | The ligand that this bound molecule refers |
previous segment | The previous molecule segment in the parent molecule |
next segment | The next molecule segment in the parent molecule |
of organism | |
has | |
has | |
segments | The segments of a molecule that are associated with other entities and database like swiss-prot etc. |
has | |
has | |
|
Reference attributes:Assembly Model Id - Naming attributes:Accession Code,Assembly Serial,Model Serial |
C:ASSEMBLY_MODEL_ID, S:10, A:4.0 | The database identifier of the Assembly Model |
C:ACCESSION_CODE, S:8, A:4.0 | The PDB accession code of the entry |
C:ASSEMBLY_SERIAL, S:38, A:2.0 | The serial identifier of the assembly in the entry |
C:MODEL_SERIAL, S:3, A:2.0 | The serial identifier of the model in the entry |
Assembly Id C:ASSEMBLY_ID, S:10, A:4.0 | The database identifier of the Assembly |
Mean B for main-chain C:B_MAIN, S:0, A:1.0 | Mean B value for the protein main-chain atoms. A lower mean Bfactor may indicate a more ordered structure. |
Mean B for side-chain C:B_SIDE, S:0, A:1.0 | Mean B value for the protein side-chain atoms. A lower mean Bfactor may indicate a more ordered structure. |
Delta Accessible Surface C:DELTA_ASA, S:0, A:3.0 | Mean Delta Accessible Surface Area per Chain. The Lee and Richards method is used for accessibility calculations. This method loops over each atom in a list, and finds the surface area in square Angstroms that is accessible to a probe sphere of a radius specified. A Probe radius of 1.40 Angstroms is used with a Zslice of 0.05 is used here. (http://pqs.ebi.ac.uk/pqs-doc/pqs-help.html#delta_asa) |
Delta Solvation Energy C:DELTA_E_SOLV, S:0, A:3.0 | Delta Solvation Energy of Folding. A solvation energy of folding calculation is carried out for the complete quaternary structure generated and for each chain that makes up the assembly. A delta solvation energy is then calculated.
see D.Eisenberg and A.D. McLachlan, Nature 319, 199-203 (1986) and L.Chiche, L.M. Gregoret, F.E. Cohen and P.A.Kollman, Proc Natl. Accad. Sci. USA, 87, 3240-3243, (1990).
A positive value for this delta solvation energy of folding may indicate and error in the generation of the quaternary structure. The more negative the value may simply indicate the more hydrophobic character of the protein-protein interfaces in the assembly.
(http://pqs.ebi.ac.uk/pqs-doc/pqs-help.html#delta_sole)
|
Entry Id C:ENTRY_ID, S:10, A:4.0 | The database identifier of the Entry |
Justification Flag C:JUSTIFICATION_FLAG, S:6, A:6.0 | (for future use). Validation information to justify assambly formation |
Model Id C:MODEL_ID, S:10, A:4.0 | The database identifier of the Model |
Morris G-Factor C:MORRIS_G, S:0, A:1.0 | The Morris G-Factor is the PROCHECK Overall average G-Factor. Ideally, scores should be above -0.5. Values below -1.0 may need investigation
(http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html) |
Number of Hydrogen Bonds C:NUM_H_BONDS, S:38, A:1.0 | The number of hydrogen bonds in the assembly |
Buried Residues C:NUM_RES_BURIED, S:38, A:2.0 | Residues where they show the most significant change in relative accessible surface area going from an isolated chain to the oligomeric state.
A true oligomer would be expected to have at least some residues of this type. The cutoff used to include residues here is that the isolated chain has a relative ASA of at least 60% (exposed) and the same residue has in the oligomeric assembly a relative ASA of less than 3% (exposed).
|
Saltbridges C:NUM_SALTBRIDGE, S:38, A:2.0 | Number of SaltBridges. Inter-Chain Salt bridges are searched for with N...O distance cutoff of less than 3.35 Angstroms and that the angle is within acceptable limits. The program calculates the hydrogen position for those target nitrogen atoms where the hydrogen position is unambiguous (ie excluding NZ on Lys and N terminus). Then Angle O...H...N is calculated. For source...oxygen hydrogen bonds, the Angle source...O--Bonded carbon is calculated. Limits on both these Angles are 115 and 85 degrees respectively. (the method used is from Tadeusz Skarzynski's ccp4 program contact.f
(http://pqs.ebi.ac.uk/pqs-doc/pqs-help.html#SaltBridge)
|
PDB Model Serial C:PDB_MODEL_SERIAL, S:3, A:2.0 | The serial of the model as was given in the PDB. Model serial is a more consistent way to identify models since in PDB these serials do not always start from 1 and sometimes get negative numbers.
So there is no simple way to get the first model of an entry. With model serial, this is always the model with serial 0. |
Percent Accessible Surface C:PERCENT_ASA, S:0, A:1.0 | Mean Percent Accessible Surface Area per Chain that is lost upon complex formation relative to the isolated chains (http://pqs.ebi.ac.uk/pqs-doc/pqs-help.html#PercentASA). |
Procheck RAMA C:RAMA, S:0, A:1.0 | The RAMA is the percent of the residues in most favoured core regions from PROCHECK (http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html) |
Release Status C:REL_STATUS, S:1, A:1.0 | A flag that specifies if the current entry is publicly released or not |
RMS-factor C:RMS, S:0, A:2.0 | This is the RMS for superposition when the aligned C-alpha coordinates are superimposed. If the RMS is less than 3.1 Angstroms, then the chains are not only chemically equivalent but accepted as symmetrically equivalent (either via crystallographic symmetry or by proper-non-crystallographic symmetry operations). The superposition method uses the algorithm given in, Hendrickson, Acta Cryst (1979) A35, 158-163. The spherical Polar Angles Phi, Psi and Chi from the rotation matrix R are also generated. The Polar Angles are as defined in Rossman and Blow (1962) Acta Cryst 15, 24-31.
The RMS factor is also used to determine if a structure is HOMO or HETERO.
The criteria for setting a structure as HOMO or HETERO is not limited to sequence homology of constituent chains. In the PQS data set a criteria for stereochemistry is also applied.
After an automatic alignment based only on ATOM records in the PDB files is applied then if the chains are equal by sequence a superposition of the equivalent C-alpha atoms is applied and the RMS derived.
Normally the superposition RMS based on C-alpha atoms should be less than 0.3 Angstroms, here a cutoff of 3.1 Angstroms is applied and chains of equal sequence that have an RMS greater than this value are set to be HETERO.
(http://pqs.ebi.ac.uk/pqs-doc/pqs-help.html)
|
Total Accessible Surface Area C:TOTAL_ASA, S:0, A:3.0 | The Total Accessible Surface Area is the absolute sum of the accessible surface |
Delta Solvation Energy C:TOTAL_E_SOLV, S:0, A:4.0 | A solvation energy of folding calculation is carried out for the complete quaternary structure generated and for each chain that makes up the assembly. A delta solvation energy is then calculated.
see D.Eisenberg and A.D. McLachlan, Nature 319, 199-203 (1986) and L.Chiche, L.M. Gregoret, F.E. Cohen and P.A.Kollman, Proc Natl. Accad. Sci. USA, 87, 3240-3243, (1990)
A positive value for this delta solvation energy of folding may indicate and error in the generation of the quaternary structure. The more negative the value may simply indicate the more hydrophobic character of the protein-protein interfaces in the assembly.
|
of | The model of the assembly model |
o | The entry of the assembly model |
of | The assembly of the assembly model |
|
Reference attributes:Atom Id - Naming attributes:Accession Code,Residue Serial,Residue PDB Code |
C:ATOM_ID, S:10, A:5.0 | The database identifier of the Atom |
C:ACCESSION_CODE, S:8, A:4.0 | The PDB accession code of the entry |
C:RESIDUE_SERIAL, S:38, A:3.0 | Serial number of the residue in the chain.
Starts with 1 for the first residue (N-terminal or 5'-terminal) in the chain, and increases by 1 with each position along the chain uniquely identifying the residue in the chain. |
Residue PDB Code  C:RESIDUE_PDB_CODE, S:3, A:1.0 | The code of the residue or ligand as was defined in the PDB. The reference ligand (chem comp) code should be used instead, since in cases where these two are different there was some error in the original PDB data that was identified during clean up.
Common cases of these are
1) The chemical structure implied by the PDB coordinates is entirely irrelevant with the ligand with this code in the chemical dictionary. A big mess in the PDB data.
2) The structure in the PDB is a structurally modified version of the ligand with this code for example an extra atom was introduced (i.e. modified aminoacids). In these cases a new ligand is defined in the chemical dictionary and is assigned to this residue or bound molecule.
3) The PDB coordinates imply a different stereoisomer. A new ligand is introduced in the chemical dictionary for the new stereoisomer. |
Atom Type C:ATOM_TYPE, S:1, A:1.0 | The atom type is used to mark special cases of atoms. In the vast majority of cases this flag has the value 'R' and this means that this has been identified and associated with one of the atoms of a known ligand or residue from the chem comp (ligand reference) dictionary.
In these cases where it has the value 'D' it denotes that this residue or ligand could not be matched either by using atom names or by graph matching with the corresponding residue or ligand in the chem comp (ligand reference) dictionary.
This is clearly a clean up issue. Either the occurence of the residue (or ligand) with this code in the PDB file had more atoms than in other PDB files, or it used different names for the atoms, and additional an attempt to match the chemical graph of the new residue (constructed by the coordinates) also failed.
Ideally with some additional effort there will not be any more 'D' atoms.
The last possibility for atom type is to get the value 'U' for 'Unknown'.
This may happen either for Q atoms from NMR entries or from cases with unobserved residues in the middle of a chain where additional (non-existing) hydrogens are added by the authors in the residues before of after the missing part to fix the valence problems. |
Chain PDB Code C:CHAIN_PDB_CODE, S:1, A:1.0 | The original code of the chain as found in the PDB. There are problems with the chain code since it is not used in a consistent way in the PDB.
Firstly in many cases this is null in cases where there is a single chain in the entry.
Additionally very often the same chain code is used both for a polymer chain and a bound molecule (that is bound to it).
So generally the PDB chain code is often not a distinct identified for a chain. For this reason the chain code was introduced which is consistent and uniform.
The purpose of the chain code is to uniquely identify a chain in an assembly. So in cases where chain A is used 4 times in an assembly, the generated chains will have chain codes A, A1, A2, A3.
Although for the chain that has been marked as non-symmetric valid (that should be used to extract the original asymmetric PDB data), then the original PDB code is used (if it is correct) i.e. A.
In these cases where a chain in the PDB did not have a chain code, then the first not used letter is reserved (i.e. A).
When 2 different chains (i.e. polymer chain and bound molecule chain) share the same PDB code, then the chain code of the bound molecule is consistently derived from the chain code of the polymer chain
|
Charge C:CHARGE, S:0, A:2.0 | The formal charge of the atom as specified in the chem comp dictionary |
Chem Atom Id C:CHEM_ATOM_ID, S:10, A:4.0 | The database identifier of the Chem Atom |
Atom Name C:CHEM_ATOM_NAME, S:8, A:3.0 | The standard PDB name of the atom in the molecule that correspond with the definition of the ligand in the chemical dictionary.
This might be different from the name in the PDB entry either due to inconsistent naming, or because this is a totally different ligand. |
Atom ordering C:CHEM_ATOM_ORDERING, S:4, A:2.0 | The standard ordering of the atom in the molecule as defined in the ligand dictionary. Atoms should always be presented based on their ordering |
PDB Atom Format Prefix C:CHEM_ATOM_NAME_PDB_LS, S:1, A:1.0 | This column includes the space(s) that have to be prefixed to the atom names in order to export them in PDB format. Spaces is atom names are not significant (ie it is not allowed to have 'CA ' and ' CA' in the same ligand or residue) but have to be preserved since many programs (like rasmol) use these spaces in order to determine the element of the atom. |
Ligand code C:CHEM_COMP_CODE, S:12, A:6.0 | The standard extended molecule code of the aminoacid or ligand. It is composed by the PDB 3 letter code with an optional topological indicator appended after an underscore |
Chem Comp Id C:CHEM_COMP_ID, S:10, A:3.0 | The database identifier of the Chem Comp |
Chirality C:CHIRALITY, S:1, A:1.0 | The stereocenter indicator denoting the chirality of the atom as specified by the molecule dictionary. R means that substituents circulate clockwise (order by lowest priority) and S counter clockwise |
Element Symbol C:ELEMENT_SYMBOL, S:15, A:2.0 | The standard one or two character symbol of the chemical element of the atom |
Entry Id C:ENTRY_ID, S:10, A:4.0 | The database identifier of the Entry |
Leaving Flag C:LEAVING_FLAG, S:1, A:1.0 | Defined in the chem comp dictionary, this flag is 'Y' if this atom is lost from the compound on formation of a common/standard link (e.g. the
linking oxygen of sugars). |
Hydrogen Donor-Acceptor C:N_H_DONOR_ACCEPTOR, S:1, A:1.0 | Defined in the chem comp dictionary this denotes the hydrogen bonding potential of the atom and takes values (D-Donor,A-Acceptor,B-Both) |
Original PDB file Atom Name C:ATOM_FILE_NAME, S:24, A:3.0 | This is the original nomenclature for the atom as it was found in the PDB file. The official name of the atom is give by "Atom Name" and it may be different since it is an important part of the clean up to make the atom nomenclatures uniform across the PDB. |
PDB Group C:PDB_GROUP, S:1, A:1.0 | Provides if the atom was defined as ATOM (A) or HETATM (H) in the PDB |
Residue PDB Insert Code C:RESIDUE_INSERT_CODE, S:1, A:1.0 | The insertion code of the residue, as was originally found in the PDB.
The residue serial should be used instead since the PDB SEQ and INSERT CODE are not consistently and uniformly used in PDB |
Residue PDB Seq C:RESIDUE_PDB_SEQ, S:4, A:3.0 | The sequence of the residue, as was originally found in the PDB (has to be used together with insert code). |
Ring Flag C:RING_FLAG, S:1, A:1.0 | Flag denoting that this atom belongs at least in one ring |
Standard Name C:STANDARD_NAME, S:12, A:2.0 | The EBI standard atom name that attempts to solve all the PDB name problems (i.e. always start with element name) |
Standard Ordering C:STANDARD_ORDERING, S:0, A:3.0 | The EBI standard ordering of the atom. Atoms should be listed in this order in any reference of the molecule, when the standard name is used |
Substruct Code C:SUBSTRUCT_CODE, S:5, A:2.0 | The chemical nature of an atom within a chemical component that assigns the atom to a substructure of the component, if appropriate.
'main' 'main chain of an amino acid'
'side' 'side chain of an amino acid'
'base' 'base of a nucleic acid'
'phos' 'phosphate of a nucleic acid'
'suga' 'sugar of a nucleic acid'
'none' 'not appropriate for this monomer'
|
reference | The reference ligand atom that the atom corresponds |
of | The entry where the atom belongs |
has | The sites involving the atomReverse relation: of of Reverse entity: Site - Relation attributes: Atom Id |
reference | The reference ligand that the atom corresponds |
|
Reference attributes:Atom Data Id - Naming attributes:Accession Code,Assembly Serial,Chain Code,Residue Serial,Ligand code,Atom Name |
C:ATOM_DATA_ID, S:0, A:6.0 | The database identifier of the Atom Data |
C:ACCESSION_CODE, S:8, A:4.0 | The PDB accession code of the entry |
C:ASSEMBLY_SERIAL, S:38, A:2.0 | The serial identifier of the assembly in the entry |
C:CHAIN_CODE, S:8, A:2.0 | The standard code of the chain that uniquely identifies it in the assembly. It is an extension of the PDB chain Id.
In cases where symmetry operations have been applied to a chain, these chains are named with a numeric suffix, ie. A,A1,A2,A3 ...
The chain id specified in the PDB file is also ignored for waters and bound molecules, and their codes are derived from the name of the chain that they are bound to.
Finally there are no "null" chain codes and in cases where no id was specified in the PDB file, then arbitrary chain codes are assigned (i.e. A,B) |
C:RESIDUE_SERIAL, S:38, A:3.0 | Serial number of the residue in the chain.
Starts with 1 for the first residue (N-terminal or 5'-terminal) in the chain, and increases by 1 with each position along the chain uniquely identifying the residue in the chain. |
C:CHEM_COMP_CODE, S:12, A:6.0 | The standard extended molecule code of the aminoacid or ligand. It is composed by the PDB 3 letter code with an optional topological indicator appended after an underscore |
C:CHEM_ATOM_NAME, S:8, A:3.0 | The standard PDB name of the atom in the molecule that correspond with the definition of the ligand in the chemical dictionary.
This might be different from the name in the PDB entry either due to inconsistent naming, or because this is a totally different ligand. |
Alt Code C:ALT_CODE, S:8, A:1.0 | The ALT code of the atom as defined in the PDB |
Alt Id C:ALT_ID, S:10, A:2.0 | The database identifier of the Alt |
Assembly Id C:ASSEMBLY_ID, S:10, A:4.0 | The database identifier of the Assembly |
Atom Id C:ATOM_ID, S:10, A:5.0 | The database identifier of the Atom |
PDB Export Chain Code C:CHAIN_CODE_1_LETTER, S:1, A:1.0 | This is an additional 1 letter code that uniquely identifies it in the assembly. It is arbitrary and its purpose is to be able to export files in PDB format |
Chain Id C:CHAIN_ID, S:10, A:5.0 | The database identifier of the Chain |
Chain PDB Code C:CHAIN_PDB_CODE, S:1, A:1.0 | The original code of the chain as found in the PDB. There are problems with the chain code since it is not used in a consistent way in the PDB.
Firstly in many cases this is null in cases where there is a single chain in the entry.
Additionally very often the same chain code is used both for a polymer chain and a bound molecule (that is bound to it).
So generally the PDB chain code is often not a distinct identified for a chain. For this reason the chain code was introduced which is consistent and uniform.
The purpose of the chain code is to uniquely identify a chain in an assembly. So in cases where chain A is used 4 times in an assembly, the generated chains will have chain codes A, A1, A2, A3.
Although for the chain that has been marked as non-symmetric valid (that should be used to extract the original asymmetric PDB data), then the original PDB code is used (if it is correct) i.e. A.
In these cases where a chain in the PDB did not have a chain code, then the first not used letter is reserved (i.e. A).
When 2 different chains (i.e. polymer chain and bound molecule chain) share the same PDB code, then the chain code of the bound molecule is consistently derived from the chain code of the polymer chain
|
Chem Atom Id C:CHEM_ATOM_ID, S:10, A:4.0 | The database identifier of the Chem Atom |
Atom ordering C:CHEM_ATOM_ORDERING, S:4, A:2.0 | The standard ordering of the atom in the molecule as defined in the ligand dictionary. Atoms should always be presented based on their ordering |
Chem Comp Id C:CHEM_COMP_ID, S:10, A:3.0 | The database identifier of the Chem Comp |
PDB Atom Format Prefix C:CHEM_ATOM_NAME_PDB_LS, S:1, A:1.0 | This column includes the space(s) that have to be prefixed to the atom names in order to export them in PDB format. Spaces is atom names are not significant (ie it is not allowed to have 'CA ' and ' CA' in the same ligand or residue) but have to be preserved since many programs (like rasmol) use these spaces in order to determine the element of the atom. |
3 Letter Code C:CODE_3_LETTER, S:3, A:3.0 | This attribute provides a code from the chem comp dictionary for standard residues.
This attribute must be the same for small molecules that represent our variations on topology/chemistry for a polymer component e.g. All ALA's should have a code_3_letter of ALA.
All adenosine nucleotides should have a 3 letter code of A, except for those that have a topology of 'free'.
This code is now obsolete and the Comp Code should be used instead in most cases |
Element Symbol C:ELEMENT_SYMBOL, S:15, A:2.0 | The standard one or two character symbol of the chemical element of the atom |
Entry Id C:ENTRY_ID, S:10, A:4.0 | The database identifier of the Entry |
Model Id C:MODEL_ID, S:10, A:4.0 | The database identifier of the Model |
Model Serial C:MODEL_SERIAL, S:3, A:2.0 | The serial identifier of the model in the entry |
Valid In Assymetric Unit C:NON_ASSEMBLY_VALID, S:1, A:1.0 | This item is to be used not only in an assembly context, but also to represent the original asymmetric unit |
Occupancy C:OCCUPANCY, S:0, A:3.0 | The fraction of the atom type present at this site. The sum of the occupancies of all the atom types at this site may not significantly exceed 1.0 unless it is a dummy site.
|
Original X C:ORIG_X, S:0, A:5.0 | The original asymmetric X coordinate of the atom |
Original Y C:ORIG_Y, S:0, A:5.0 | The original asymmetric Y coordinate of the atom |
Original Z C:ORIG_Z, S:0, A:5.0 | The original asymmetric Z coordinate of the atom |
PDB Charge C:PDB_CHARGE, S:10, A:1.0 | The atomic charge originally used where this entry was included as a PDB-format file
|
PDB Element C:PDB_ELEMENT, S:2, A:2.0 | The symbol of the element as was originally found in the PDB |
PDB Group C:PDB_GROUP, S:1, A:1.0 | Provides if the atom was defined as ATOM (A) or HETATM (H) in the PDB |
PDB Model Serial C:PDB_MODEL_SERIAL, S:3, A:2.0 | The serial of the model as was given in the PDB. Model serial is a more consistent way to identify models since in PDB these serials do not always start from 1 and sometimes get negative numbers.
So there is no simple way to get the first model of an entry. With model serial, this is always the model with serial 0. |
Residue Id C:RESIDUE_ID, S:0, A:5.0 | The database identifier of the Residue |
Residue PDB Insert Code C:RESIDUE_PDB_INSERT_CODE, S:1, A:1.0 | The insertion code of the residue, as was originally found in the PDB.
The residue serial should be used instead since the PDB SEQ and INSERT CODE are not consistently and uniformly used in PDB |
Residue PDB Seq C:RESIDUE_PDB_SEQ, S:4, A:3.0 | The sequence of the residue, as was originally found in the PDB (has to be used together with insert code). |
Residue Type C:RESIDUE_TYPE, S:1, A:1.0 | The type of the component R:residue, B:bound molecule, W:water. This normally has to correspond with the type of the chain where there residue belongs |
Serial C:SERIAL, S:0, A:4.0 | A serial number of the atom in the assymetric unit. A more appropriate way to order atoms is by the combination of "residue serial" and "atom ordering" |
Isotropic displacement C:U_ISO_OR_EQUIV, S:0, A:4.0 | Isotropic atomic displacement parameter, or equivalent isotropic atomic displacement parameter, U~equiv~, calculated from anisotropic atomic displacement parameters.
U~equiv~ = (1/3) sum~i~[sum~j~(U~ij~ A~i~ A~j~ a*~i~ a*~j~)]
A = the real space cell lengths
a* = the reciprocal space cell lengths
Ref: Fischer, R. X. & Tillmanns, E. (1988). Acta Cryst. C44,775-776.
|
Wyckoff Symbol C:WYCKOFF_SYMBOL, S:1, A:1.0 | The Wyckoff symbol (letter) as listed in the space-group section of International Tables for Crystallography, Vol. A (1987). Is empty ???
|
X C:X, S:0, A:7.0 | The X coordinate of the atom, after the symmetry transformation has been applied in the assembly |
Y C:Y, S:0, A:7.0 | The Y coordinate of the atom, after the symmetry transformation has been applied in the assembly |
Z C:Z, S:0, A:7.0 | The Z coordinate of the atom, after the symmetry transformation has been applied in the assembly |
main neighbour of | |
of residue | |
of | The assembly where the atom belongs |
of | The entry where the atom belongs |
1st end | |
2nd end | |
alternative | The alternative coordinates givem for these atom coordinatesReverse relation: has of Reverse entity: Alt - Relation attributes: Alt Id |
has | The sites involving the atom coordinates |
2nd begin | |
1st begin | |
reference | The reference ligand atom that the atom corresponds |
in chain | |
|
Reference attributes:Chain Seq Alignment Id - Naming attributes:Accession Code,Aligned Accession Code,Chain Code,Aligned Chain Code |
C:CHAIN_SEQ_ALIGNMENT_ID, S:10, A:5.0 | The database identifier of the Chain Seq Alignment |
Entry Id C:ENTRY_ID, S:10, A:4.0 | The database identifier of the Entry |
Aligned Entry Id C:ALIGNED_ENTRY_ID, S:10, A:4.0 | The database identifier of the Aligned Entry |
C:CHAIN_CODE, S:8, A:1.0 | The standard code of the chain that uniquely identifies it in the assembly. |
C:ALIGNED_CHAIN_CODE, S:8, A:1.0 | The standard code of the Aligned Chain |
C:ACCESSION_CODE, S:8, A:4.0 | The PDB accession code of the entry |
C:ALIGNED_ACCESSION_CODE, S:8, A:4.0 | The PDB accession code of the aligned entry |
Aligned Chain Id C:ALIGNED_CHAIN_ID, S:10, A:4.0 | The database identifier of the Aligned Chain |
Aligned Chain PDB Code C:ALIGNED_CHAIN_PDB_CODE, S:1, A:1.0 | PDB code of the aligned chain |
Alignment Type C:ALIGNMENT_TYPE, S:3, A:3.0 | The type of the alignment. For sequence (FASTA) alignments is 'SEQ' |
Accessible Surface Area C:ASA, S:0, A:4.0 | Accessible surface area of the chain in the assembly |
Assembly Id C:ASSEMBLY_ID, S:10, A:4.0 | The database identifier of the Assembly |
Assembly Serial C:ASSEMBLY_SERIAL, S:38, A:2.0 | The serial identifier of the assembly in the entry |
PDB Export Chain Code C:CHAIN_CODE_1_LETTER, S:1, A:1.0 | This is an additional 1 letter code that uniquely identifies it in the assembly. It is arbitrary and its purpose is to be able to export files in PDB format |
Chain Id C:CHAIN_ID, S:10, A:4.0 | The database identifier of the Chain |
PDB Export Residue Increment C:CHAIN_INCR_1_LETTER, S:0, A:1.0 | There are a few cases where there are more chains that the 1 letter code may uniquely identify (more than 52). In these cases, the same 1 letter is reused, but an increment is added to the PDB sequence of their residues (i.e. A with residues 1..100 and chain A with increment 10000 and residues 10000..10100 |
Chain Msd Code C:CHAIN_MSD_CODE, S:8, A:5.0 | An internal longer code for a chain (defined by MSD) that includes the type of the chain (protein, bound molecule etc). It does not identify uniquely a chain in an assembly; the chain code has to be used instead |
Chain PDB Code C:CHAIN_PDB_CODE, S:1, A:1.0 | The original code of the chain as found in the PDB. There are problems with the chain code since it is not used in a consistent way in the PDB.
Firstly in many cases this is null in cases where there is a single chain in the entry.
Additionally very often the same chain code is used both for a polymer chain and a bound molecule (that is bound to it).
So generally the PDB chain code is often not a distinct identified for a chain. For this reason the chain code was introduced which is consistent and uniform.
The purpose of the chain code is to uniquely identify a chain in an assembly. So in cases where chain A is used 4 times in an assembly, the generated chains will have chain codes A, A1, A2, A3.
Although for the chain that has been marked as non-symmetric valid (that should be used to extract the original asymmetric PDB data), then the original PDB code is used (if it is correct) i.e. A.
In these cases where a chain in the PDB did not have a chain code, then the first not used letter is reserved (i.e. A).
When 2 different chains (i.e. polymer chain and bound molecule chain) share the same PDB code, then the chain code of the bound molecule is consistently derived from the chain code of the polymer chain
|
Chain Type C:CHAIN_TYPE, S:1, A:1.0 | The type of the chain (polymer C,non-polymer B,water W) |
Details C:DETAILS, S:2000, A:1.0 | A description of special aspects of the chain entity. Is empty ??? |
Chain Accessible Surface Area C:DGAC_ASA, S:0, A:1.0 | Accessible surface area of the chain in the assembly ??? |
Chain Solvation Energy C:DGAC_SOLE, S:0, A:1.0 | Solvation energy of the chain ??? |
Matrix Id C:MATRIX_ID, S:0, A:4.0 | The database identifier of the Matrix |
Valid In Assymetric Unit C:NON_ASSEMBLY_VALID, S:1, A:1.0 | This item is to be used not only in an assembly context, but also to represent the original asymmetric unit |
Number of Residues C:NUM_RESIDUES, S:8, A:3.0 | The number of residues in the chain |
Sequence Alignment Version C:SEQ_ALIGNMENT_VERSION, S:3, A:1.0 | The version of the sequence alignment algorithm |
Similarity C:SIMILARITY, S:8, A:2.0 | The sequence alignment entity includes alignments that have a similarity higher from the predefined cut-off. The similarity score is a number from 0 - 100 that is based on the normalized "z-scores" of the FASTA algorithm (http://www.ebi.ac.uk/fasta33/fasta3x.txt) |
Solvation energy C:SOLE, S:0, A:4.0 | Solvation energy of the chain |
Symm Asym Id C:SYMM_ASYM_ID, S:8, A:6.0 | symm_asym identifier |
of | |
of | |
aligned | |
of | |
aligned | |
of | |
|
Reference attributes:Chain Str Alignment Id - Naming attributes:Accession Code,Aligned Accession Code,Chain Code,Aligned Chain Code |
C:CHAIN_STR_ALIGNMENT_ID, S:10, A:5.0 | The database identifier of the Chain Str Alignment |
C:ACCESSION_CODE, S:8, A:4.0 | The PDB accession code of the entry |
C:ALIGNED_ACCESSION_CODE, S:8, A:4.0 | The PDB accession code of the aligned entry |
C:CHAIN_CODE, S:8, A:1.0 | The standard code of the chain that uniquely identifies it in the assembly. |
C:ALIGNED_CHAIN_CODE, S:8, A:1.0 | The standard code of the Aligned Chain |
Aligned Chain Id C:ALIGNED_CHAIN_ID, S:10, A:5.0 | The database identifier of the Aligned Chain |
Aligned Chain PDB Code C:ALIGNED_CHAIN_PDB_CODE, S:1, A:1.0 | PDB code of the aligned chain |
Aligned Entry Id C:ALIGNED_ENTRY_ID, S:10, A:4.0 | The database identifier of the Aligned Entry |
Alignment Type C:ALIGNMENT_TYPE, S:3, A:3.0 | The type of the alignment. For structural alignments is 'STR' |
Superposition Vector 1 C:AM1, S:0, A:11.0 | Element of the matrix of the superposition transformation operation, that may be used to superimpose the 2 chains |
Superposition Matrix 11 C:AM11, S:0, A:10.0 | Element of the matrix of the superposition transformation operation, that may be used to superimpose the 2 chains |
Superposition Matrix 12 C:AM12, S:0, A:10.0 | Element of the matrix of the superposition transformation operation, that may be used to superimpose the 2 chains |
Superposition Matrix 13 C:AM13, S:0, A:10.0 | Element of the matrix of the superposition transformation operation, that may be used to superimpose the 2 chains |
Superposition Vector 2 C:AM2, S:0, A:11.0 | Element of the matrix of the superposition transformation operation, that may be used to superimpose the 2 chains |
Superposition Matrix 21 C:AM21, S:0, A:10.0 | Element of the matrix of the superposition transformation operation, that may be used to superimpose the 2 chains |
Superposition Matrix 22 C:AM22, S:0, A:10.0 | Element of the matrix of the superposition transformation operation, that may be used to superimpose the 2 chains |
Superposition Matrix 23 C:AM23, S:0, A:10.0 | Element of the matrix of the superposition transformation operation, that may be used to superimpose the 2 chains |
Superposition Vector 3 C:AM3, S:0, A:11.0 | Element of the matrix of the superposition transformation operation, that may be used to superimpose the 2 chains |
Superposition Matrix 31 C:AM31, S:0, A:10.0 | Element of the matrix of the superposition transformation operation, that may be used to superimpose the 2 chains |
Superposition Matrix 32 C:AM32, S:0, A:10.0 | Element of the matrix of the superposition transformation operation, that may be used to superimpose the 2 chains |
Superposition Matrix 33 C:AM33, S:0, A:10.0 | Element of the matrix of the superposition transformation operation, that may be used to superimpose the 2 chains |
Accessible Surface Area C:ASA, S:0, A:4.0 | Accessible surface area of the chain in the assembly |
Assembly Id C:ASSEMBLY_ID, S:10, A:4.0 | The database identifier of the Assembly |
Assembly Serial C:ASSEMBLY_SERIAL, S:38, A:2.0 | The serial identifier of the assembly in the entry |
PDB Export Chain Code C:CHAIN_CODE_1_LETTER, S:1, A:1.0 | This is an additional 1 letter code that uniquely identifies it in the assembly. It is arbitrary and its purpose is to be able to export files in PDB format |
Chain Id C:CHAIN_ID, S:10, A:5.0 | The database identifier of the Chain |
PDB Export Residue Increment C:CHAIN_INCR_1_LETTER, S:0, A:1.0 | There are a few cases where there are more chains that the 1 letter code may uniquely identify (more than 52). In these cases, the same 1 letter is reused, but an increment is added to the PDB sequence of their residues (i.e. A with residues 1..100 and chain A with increment 10000 and residues 10000..10100 |
Chain Msd Code C:CHAIN_MSD_CODE, S:8, A:5.0 | An internal longer code for a chain (defined by MSD) that includes the type of the chain (protein, bound molecule etc). It does not identify uniquely a chain in an assembly; the chain code has to be used instead |
Chain PDB Code C:CHAIN_PDB_CODE, S:1, A:1.0 | The original code of the chain as found in the PDB. There are problems with the chain code since it is not used in a consistent way in the PDB.
Firstly in many cases this is null in cases where there is a single chain in the entry.
Additionally very often the same chain code is used both for a polymer chain and a bound molecule (that is bound to it).
So generally the PDB chain code is often not a distinct identified for a chain. For this reason the chain code was introduced which is consistent and uniform.
The purpose of the chain code is to uniquely identify a chain in an assembly. So in cases where chain A is used 4 times in an assembly, the generated chains will have chain codes A, A1, A2, A3.
Although for the chain that has been marked as non-symmetric valid (that should be used to extract the original asymmetric PDB data), then the original PDB code is used (if it is correct) i.e. A.
In these cases where a chain in the PDB did not have a chain code, then the first not used letter is reserved (i.e. A).
When 2 different chains (i.e. polymer chain and bound molecule chain) share the same PDB code, then the chain code of the bound molecule is consistently derived from the chain code of the polymer chain
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Chain Type C:CHAIN_TYPE, S:1, A:1.0 | The type of the chain (polymer C,non-polymer B,water W) |
Details C:DETAILS, S:2000, A:1.0 | A description of special aspects of the chain entity. Is empty ??? |
Chain Accessible Surface Area C:DGAC_ASA, S:0, A:1.0 | Accessible surface area of the chain in the assembly ??? |
Chain Solvation Energy C:DGAC_SOLE, S:0, A:1.0 | Solvation energy of the chain ??? |
Entry Id C:ENTRY_ID, S:10, A:4.0 | The database identifier of the Entry |
Length of Alignment C:LENGTH, S:8, A:3.0 | Length of alignment Nalgn, or number of matched residues, is calculated at best 3D superposition of query and target structures. The residues are aligned in 3D on the basis of their spatial closeness. The orientation of the structures is optimized such as to minimize RPDBe and to maximize the number of aligned residues.
(http://www.ebi.ac.uk/msd-srv/ssm/ssmresults.html)
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Matrix Id C:MATRIX_ID, S:0, A:4.0 | The database identifier of the Matrix |
Model Serial C:MODEL_SERIAL, S:3, A:2.0 | The serial identifier of the model in the entry |
Valid In Assymetric Unit C:NON_ASSEMBLY_VALID, S:1, A:1.0 | This item is to be used not only in an assembly context, but also to represent the original asymmetric unit |
Number of Residues C:NUM_RESIDUES, S:8, A:3.0 | The number of residues in the chain |
RMSD C:RMSD, S:0, A:8.0 | RPDBe stands for the Root Mean Square Deviation, calculated between Ca-atoms of matched residues at best 3D superposition of the query and target structures. RPDBe is presented in angstroms. In simple words, RPDBe gives you an idea how separated, at best 3D superposition, a "typical" pair of matched Ca-atoms is. Generally, the larger RMSD, the more distant the matched structures are.
(http://www.ebi.ac.uk/msd-srv/ssm/ssmresults.html)
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Solvation energy C:SOLE, S:0, A:4.0 | Solvation energy of the chain |
Structural Alignment Version C:STR_ALIGNMENT_VERSION, S:3, A:1.0 | The version of the structural alignment algorithm |
Symm Asym Id C:SYMM_ASYM_ID, S:8, A:6.0 | The database identifier of the Symm Asym |
of | |
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aligned | |
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aligned | |
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Reference attributes:Residue Id - Naming attributes:Accession Code,Assembly Serial,Chain Code,Residue Serial |
C:RESIDUE_ID, S:0, A:5.0 | The database identifier of the Residue |
C:ACCESSION_CODE, S:8, A:4.0 | The PDB accession code of the entry |
C:ASSEMBLY_SERIAL, S:38, A:2.0 | The serial identifier of the assembly in the entry |
C:CHAIN_CODE, S:8, A:2.0 | The standard code of the chain that uniquely identifies it in the assembly. It is an extension of the PDB chain Id.
In cases where symmetry operations have been applied to a chain, these chains are named with a numeric suffix, ie. A,A1,A2,A3 ...
The chain id specified in the PDB file is also ignored for waters and bound molecules, and their codes are derived from the name of the chain that they are bound to.
Finally there are no "null" chain codes and in cases where no id was specified in the PDB file, then arbitrary chain codes are assigned (i.e. A,B) |
C:SERIAL, S:38, A:3.0 | Serial number of the residue in the chain.
Starts with 1 for the first residue (N-terminal or 5'-terminal) in the chain, and increases by 1 with each position along the chain uniquely identifying the residue in the chain. |
Assembly Id C:ASSEMBLY_ID, S:10, A:4.0 | The database identifier of the Assembly |
PDB Export Chain Code C:CHAIN_CODE_1_LETTER, S:1, A:1.0 | This is an additional 1 letter code that uniquely identifies it in the assembly. It is arbitrary and its purpose is to be able to export files in PDB format |
Chain Id C:CHAIN_ID, S:10, A:5.0 | The database identifier of the Chain |
Chain Msd Code C:CHAIN_MSD_CODE, S:8, A:5.0 | An internal longer code for a chain (defined by MSD) that includes the type of the chain (protein, bound molecule etc). It does not identify uniquely a chain in an assembly; the chain code has to be used instead |
Chain PDB Code C:CHAIN_PDB_CODE, S:1, A:1.0 | The original code of the chain as found in the PDB. There are problems with the chain code since it is not used in a consistent way in the PDB.
Firstly in many cases this is null in cases where there is a single chain in the entry.
Additionally very often the same chain code is used both for a polymer chain and a bound molecule (that is bound to it).
So generally the PDB chain code is often not a distinct identified for a chain. For this reason the chain code was introduced which is consistent and uniform.
The purpose of the chain code is to uniquely identify a chain in an assembly. So in cases where chain A is used 4 times in an assembly, the generated chains will have chain codes A, A1, A2, A3.
Although for the chain that has been marked as non-symmetric valid (that should be used to extract the original asymmetric PDB data), then the original PDB code is used (if it is correct) i.e. A.
In these cases where a chain in the PDB did not have a chain code, then the first not used letter is reserved (i.e. A).
When 2 different chains (i.e. polymer chain and bound molecule chain) share the same PDB code, then the chain code of the bound molecule is consistently derived from the chain code of the polymer chain
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Ligand code C:CHEM_COMP_CODE, S:12, A:5.0 | The standard extended molecule code of the aminoacid or ligand. It is composed by the PDB 3 letter code with an optional topological indicator appended after an underscore |
Chem Comp Id C:CHEM_COMP_ID, S:0, A:3.0 | The database identifier of the Chem Comp |
Code 1 Letter C:CODE_1_LETTER, S:5, A:1.0 | One code letter for the ligand (aminoacid, nucleic acid) in order to construct sequences. |
3 Letter Code C:CODE_3_LETTER, S:3, A:3.0 | This attribute provides a code from the chem comp dictionary for standard residues.
This attribute must be the same for small molecules that represent our variations on topology/chemistry for a polymer component e.g. All ALA's should have a code_3_letter of ALA.
All adenosine nucleotides should have a 3 letter code of A, except for those that have a topology of 'free'.
This code is now obsolete and the Comp Code should be used instead in most cases |
Entry Id C:ENTRY_ID, S:10, A:4.0 | The database identifier of the Entry |
Molecule Code C:MOLECULE_CODE, S:255, A:3.0 | Uniquely identifies a molecule in an entry. It does not need be a number; it can be any unique identifier.
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Molecule Engineered C:MOLECULE_ENGINEERED, S:1, A:1.0 | |
Molecule Id C:MOLECULE_ID, S:10, A:4.0 | The database identifier of the Molecule |
Molecule Parent Id C:MOLECULE_PARENT_ID, S:10, A:3.0 | The database identifier of the Molecule Parent |
Ncbi Tax Id C:NCBI_TAX_ID, S:15, A:3.0 | The NCBI taxonomy identifier (taxid) that points to a node of the taxonomy tree |
Valid In Assymetric Unit C:NON_ASSEMBLY_VALID, S:1, A:1.0 | This item is to be used not only in an assembly context, but also to represent the original asymmetric unit |
Not Observed C:NOT_OBSERVED, S:1, A:1.0 | The residue's coordinates are not available because the residue was not observed in the experiment data. There are no coordinates for any of its atoms. |
PDB Code C:PDB_CODE, S:3, A:3.0 | The molecule code as was originally found in PDB |
PDB Insert Code C:PDB_INSERT_CODE, S:1, A:1.0 | The insertion code is commonly used in sequence numbering and is described here. In most cases, the amino acids that comprise a protein are numbered sequentially starting with 1. However, there are a number of situations that may give rise to different numbering schemes: 1.Homologous proteins can exist in a number of different species. Depositors may use a residue numbering scheme in order to preserve the homology. The reference protein may be numbered sequentially starting with 1, then the homologous protein from another species aligned to it. If residues are not present in the homologous sequence, residue numbers may be skipped so that alignment can be preserved. If additional residues are present relative to the reference protein, they may have a letter, called an insertion code, appended to the sequence number. Negative numbers and zeros are permitted if they are needed to align the N-terminus 2.The numbering of a proenzyme may be used for the enzyme following cleavage. 3.The molecule studied might be a portion of the whole protein. The residue numbering scheme could show the relationship to the intact protein. 4.The protein might be a mutant with residues inserted and deleted. As above, the residue numbering of the native protein could be preserved by appropriate use of gaps in the numbering and/or insertion codes. 5.The nucleic acid community generally numbers structures sequentially. For double-stranded nucleic acids, entries usually use two different chain identifiers. For example, an octameric duplex would be numbered 1 - 8 for chain A, and 9 - 16 for chain B. |
PDB SEQ C:PDB_SEQ, S:4, A:3.0 | The sequence of the residue, as was originally found in the PDB (has to be used together with insert code). |
Residue Type C:RESIDUE_TYPE, S:1, A:1.0 | The type of the component R:residue, B:bound molecule, W:water. This normally has to correspond with the type of the chain where there residue belongs |
of | |
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neighbour | |
has | |
has | |
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ligand | |
has | |
has | |
2nd oxygen donor | |
1st oxygen donor | |
2nd hydrogen acceptor | |
1st hydrogen acceptor | |
has | |
has | The active site plane centers of the residue |
refers | The ligand that is the reference of the residue |
of | The assembly of the residue |
has | |
of | The PDB entry where the residue belongs |
has | |
The attribute is a part of the reference key of an instance
Entity Details: A=Number of attributes of the Entity
R=Number of relations of the Entity
T=Name of the database table
I=Approximation of the number of instances of the entity