|
|
| Swiss-Prot link per Chain A:7, R:4, T:SWP_CHAIN, I:0
| Links to Swiss-prot protein sequence database (http://www.ebi.ac.uk/swissprot/) on the chain level |
| EC Enzyme Database A:6, R:2, T:EC_MAPPING, I:11600
| Links to the EC enzyme database (http://ca.expasy.org/enzyme/) and Swiss-Prot on the molecule level |
| PubMed Citation Database A:4, R:1, T:PUBMEDLIST, I:30800
| Links to the PubMed database that provides access to millions of MEDLINE citations (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed) on the entry level |
| SCOP per chain A:6, R:2, T:SCOP_INT, I:8800000
| Links to SCOP database (http://nar.oupjournals.org/cgi/content/full/30/1/264) for structural classification of proteins (http://scop.mrc-lmb.cam.ac.uk/scop/) on the chain level |
| CATH per chain A:6, R:2, T:CATH_INT, I:9040000
| Links to the CATH Protein Structure Classification database (http://www.biochem.ucl.ac.uk/bsm/cath/) on a detailed chain level |
| PFAM per chain A:5, R:2, T:PFAM_INT, I:0
| Links to the PFAM database of protein families and profile hidden markov models (http://nar.oupjournals.org/cgi/content/full/32/suppl_1/D138) , (http://nar.oupjournals.org/cgi/content/full/30/1/276?ijkey=wfgjAWVRY.wto&keytype=ref&siteid=nar) on the chain level
(http://www.sanger.ac.uk/Software/Pfam/help/index.shtml) |
| GO Gene Ontology A:5, R:1, T:GO_SWP_MAPPING, I:311000
| Links to the GO gene ontology database (http://www.geneontology.org/) and Interpro database on the entry level |
| Interpro Protein Family A:5, R:1, T:INT_SWP_MAPPING, I:262000
| Links to the Interpro database of protein families, domains and functional sites (http://www.ebi.ac.uk/interpro/) on the chain level |
| Representative Entries A:5, R:1, T:REPRESENTATIVE, I:7620
| Grouping of entries in set of representative entries for various purposes (ie SCOP, DALI).
This is very convinient in research or statistics operations because it resolves the effect
from the existence of many structures of the same or similar proteins in the PDB that can bias such results |
| Related Entry A:7, R:2, T:RELATED_ENTRY, I:27200
| Entries that are related in some way (type of relation) |
| Swiss-Prot link per Entry A:4, R:3, T:SP_MAP_INT, I:0
| Links to Swiss-prot protein sequence database (http://www.ebi.ac.uk/swissprot/) on the entry level |
| Swiss-Prot description A:2, R:3, T:SP_DESCRIPTION, I:0
| Descriptions provided by Swissprot database |
| Swiss-Prot keyword A:2, R:3, T:SP_KEYWORD, I:0
| Keywords referred in Swissprot database |
| Swiss-Prot Protein Knowledgebase A:28, R:7, T:SWISS_PROT_MAPPING, I:9950000
| Links to Swiss-prot protein sequence database (http://www.ebi.ac.uk/swissprot/) on the very detailed residue level |
| SCOP Structural Classification of Proteins A:31, R:5, T:SCOP_MAPPING, I:8800000
| Links to SCOP database (http://nar.oupjournals.org/cgi/content/full/30/1/264) for structural classification of proteins (http://scop.mrc-lmb.cam.ac.uk/scop/) on the residue level |
| CATH Protein Structure Classification A:29, R:5, T:CATH_MAPPING, I:9040000
| Links to the CATH Protein Structure Classification database (http://www.biochem.ucl.ac.uk/bsm/cath/) on a detailed residue level |
| PFAM per Residue A:30, R:5, T:PFAM_MAPPING, I:0
| Links to the PFAM database of protein families and profile hidden markov models (http://nar.oupjournals.org/cgi/content/full/32/suppl_1/D138) , (http://nar.oupjournals.org/cgi/content/full/30/1/276?ijkey=wfgjAWVRY.wto&keytype=ref&siteid=nar) on the detailed residue level
(http://www.sanger.ac.uk/Software/Pfam/help/index.shtml)
|
| PFAM Protein Family A:9, R:1, T:PFAM_SWP_MAPPING, I:262000
| Links to the Pfam database of protein families and hidden markov models (http://nar.oupjournals.org/cgi/content/full/30/1/276?ijkey=wfgjAWVRY.wto&keytype=ref&siteid=nar) on the chain level |
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Reference attributes:Chain Id,SwissProt accession - Naming attributes:Accession Code,Chain Code,SwissProt accession |
C:CHAIN_ID, S:10, A:0.0 | The database identifier of the Chain |
C:SP_PRIMARY_ID, S:15, A:0.0 | The accession number (AC) associated with a swissprot entry (http://ca.expasy.org/sprot/userman.html#AC_line) |
Swissprot entry   C:SP_SECONDARY_ID, S:255, A:0.0 | Swissprot entry name: The first item on the ID line is the entry name of the sequence. This name is a useful means of identifying a sequence (http://ca.expasy.org/sprot/userman.html#ID_line)
|
C:ACCESSION_CODE, S:8, A:0.0 | The PDB accession code of the entry |
C:CHAIN_CODE, S:8, A:0.0 | 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) |
Chain PDB Code C:CHAIN_PDB_CODE, S:1, A:0.0 | 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
|
Entry Id   C:ENTRY_ID, S:10, A:0.0 | The database identifier of the Entry |
has    | |
has | |
for    | |
for | |
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Reference attributes:CATH domain name,Chain Id - Naming attributes:Accession Code,Chain Code,CATH superfamily code |
C:CHAIN_ID, S:10, A:5.0 | The database identifier of the Chain |
C:CHAIN_CODE, S:24, 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) |
Entry Id C:ENTRY_ID, S:10, A:4.0 | The database identifier of the Entry |
C:ACCESSION_CODE, S:24, A:4.0 | The PDB accession code of the entry |
C:CATH_ID, S:18, A:6.0 | Cath Domain Names: MUST be SIX characters (e.g. 1cuk03).
CHARACTERS 1-4: PDB Code: The first 4 characters determine the PDB code e.g. 1cuk
CHARACTER 5: Chain Character: This determines which PDB chain is represented.A chain character of zero ('0') indicates that the PDB file has no chain field.
CHARACTER 6: Domain Number: A domain number of ZERO ('0') indicates that the domain is a whole PDB chain.
(http://www.biochem.ucl.ac.uk/bsm/cath/formats/CathList.html)
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C:CATHCODE, S:45, A:11.0 | CATH superfamily code that provide information about the CATH hierarchy.
(http://www.biochem.ucl.ac.uk/bsm/cath/cath_info.html)
The hierarchy is build up by the following levels
- Architecture, A-level: This describes the overall shape of the domain structure as determined by the orientations of the secondary structures but ignores the connectivity between the secondary structures.
- Topology (Fold family), T-level: Structures are grouped into fold families at this level depending on both the overall shape and connectivity of the secondary structures.
- Homologous Superfamily, H-level: This level groups together protein domains which are thought to share a common ancestor and can therefore be described as homologous.
- Sequence families, S-level: Structures within each H-level are further clustered on sequence identity.
(http://www.biochem.ucl.ac.uk/bsm/cath/formats/CathDomainDescriptionFile.html)
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for | |
for | |
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Reference attributes:Swp Mapping Id - Naming attributes:Accession Code,Assembly Serial,Chain Code,Residue Serial,SwissProt accession |
C:SWP_MAPPING_ID, S:0, A:5.0 | The database identifier of the Swp Mapping |
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:SP_PRIMARY_ID, S:15, A:7.0 | The accession number (AC) associated with a swissprot entry (http://ca.expasy.org/sprot/userman.html#AC_line) |
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:4.0 | 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
|
Ligand code C:CHEM_COMP_CODE, S:12, A:7.0 | 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 |
Cif Serial C:CIF_SERIAL, S:8, A:1.0 | (obsolete) |
Code 1 Letter C:CODE_1_LETTER, S:5, A:1.0 | One code letter for the residue as specified in the PDB sequence and structure. |
Conflict Type C:CONFLICT_TYPE, S:255, A:2.0 | It marks and classifies conflicts between the PDBe (PDB) and Swiss-prot (for future use) |
Segment location C:DSC_TYPE, S:3, A:3.0 | Provides information about the location of the residue on the mapped segment with swiss-prot (ie begining, end) |
Entry Id C:ENTRY_ID, S:10, A:4.0 | The database identifier of the Entry |
Molecule Id C:MOLECULE_ID, S:10, A:4.0 | The database identifier of the Molecule |
Ncbi Tax Id C:NCBI_TAX_ID, S:15, A:4.0 | 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. |
Residue Id  C:RESIDUE_ID, S:0, A:5.0 | The database identifier of the Residue |
Residue PDB Code C:RESIDUE_PDB_CODE, S:3, A:3.0 | 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. |
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 |
Swissprot entry C:SP_SECONDARY_ID, S:255, A:10.0 | Swissprot entry name: The first item on the ID line is the entry name of the sequence. This name is a useful means of identifying a sequence (http://ca.expasy.org/sprot/userman.html#ID_line)
|
Swissprot residue serial C:SP_SERIAL, S:10, A:3.0 | The serial identifier of the residue in the swiss-prot sequence.
This does not correspond to the PDB residue serial because often only partial fragments of the actual
sequence are involved and observed in the PDB experiment |
SwissProt 1 Letter Code C:SP_1_LETTER_CODE, S:1, A:1.0 | This is the 1 letter code of the aminoacid as specified in the Swiss-prot database.
This can be different from the code in the PDB in very few cases where for several reasons the
protein sequence and the actual structure observed in the experiment deviate. |
has | |
for | |
for | |
for | |
for | |
for | |
has | |
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Reference attributes:Scop Mapping Id - Naming attributes:Accession Code,Assembly Serial,Chain Code,Residue Serial,Sccs,Scop sunid |
C:SCOP_MAPPING_ID, S:0, A:5.0 | The database identifier of the Scop Mapping |
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. |
Scop Id C:SCOP_ID, S:8, A:7.0 | The old scop identifier (sid) (http://scop.bic.nus.edu.sg/release-notes.html) |
Assembly Id C:ASSEMBLY_ID, S:10, A:4.0 | The database identifier of the Assembly |
Begin residue C:BEG_RES, S:8, A:2.0 | The PDB seq of the first residue of the chain segment that belongs in the same mapping with this SCOP domain |
Chain C:CHAIN, S:15, A:1.0 | This field contains the chain identifier as in the original scop data,
it should be the same as in the CHAIN_PDB_CODE , except in cases that,
this particular entry has been cleaned up |
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 |
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
|
Ligand code C:CHEM_COMP_CODE, S:12, A:7.0 | 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 |
Code 1 Letter C:CODE_1_LETTER, S:5, A:1.0 | One code letter for the residue as specified in the PDB sequence and structure. |
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 |
End Residue C:END_RES, S:8, A:2.0 | The PDB seq of the last residue of the chain segment that belongs in the same mapping with this SCOP domain |
Entry Id C:ENTRY_ID, S:0, A:4.0 | The database identifier of the Entry |
Ncbi Tax Id C:NCBI_TAX_ID, S:15, A:4.0 | 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 |
Order In C:ORDER_IN, S:0, A:2.0 | The serial of the mapping to a cath domain when 2 different segments of the same chain map to the same SCOP domain |
PDB Insert Code C:PDB_INSERT_CODE, S:1, A:1.0 | The insertion code of the residue, as was originally found in the PDB. |
Residue Id C:RESIDUE_ID, S:0, A:5.0 | The database identifier of the Residue |
Residue PDB Code C:RESIDUE_PDB_CODE, S:3, A:3.0 | 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. |
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). |
C:SCCS, S:20, A:8.0 | Scop family identifier |
Swissprot entry C:SP_SECONDARY_ID, S:1, A:1.0 | Swissprot entry name: The first item on the ID line is the entry name of the sequence. This name is a useful means of identifying a sequence (http://ca.expasy.org/sprot/userman.html#ID_line)
|
SwissProt accession C:SP_PRIMARY_ID, S:15, A:6.0 | The accession number (AC) associated with a swissprot entry (http://ca.expasy.org/sprot/userman.html#AC_line) |
Swissprot residue serial C:SP_SERIAL, S:0, A:3.0 | The serial identifier of the residue in the swiss-prot sequence.
This does not correspond to the PDB residue serial because often only partial fragments of the actual
sequence are involved and observed in the PDB experiment |
C:SUNID, S:0, A:4.0 | A number which uniquely identifies each entry in the SCOP hierarchy, including leaves and entries corresponding to the protein level
(http://scop.mrc-lmb.cam.ac.uk/scop/release-notes.html#sunid) |
SwissProt 1 Letter Code C:SP_1_LETTER_CODE, S:0, A:0.0 | This is the 1 letter code of the aminoacid as specified in the Swiss-prot database.
This can be different from the code in the PDB in very few cases where for several reasons the
protein sequence and the actual structure observed in the experiment deviate. |
of organism | |
for | |
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Reference attributes:Cath Mapping Id - Naming attributes:Accession Code,Assembly Serial,Chain Code,Residue Serial,Ligand code,CATH domain name |
C:CATH_MAPPING_ID, S:0, A:5.0 | |
Assembly Id C:ASSEMBLY_ID, S:10, A:4.0 | The database identifier of the Assembly |
C:ASSEMBLY_SERIAL, S:38, A:2.0 | The serial identifier of the assembly in the entry |
Residue Id C:RESIDUE_ID, S:0, A:5.0 | The database identifier of the Residue |
Ncbi Tax Id C:NCBI_TAX_ID, S:15, A:4.0 | The NCBI taxonomy identifier (taxid) that points to a node of the taxonomy tree |
Chain Id C:CHAIN_ID, S:10, A:5.0 | The database identifier of the Chain |
C:CHAIN_CODE, S:24, 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) |
Chain Msd Code C:CHAIN_MSD_CODE, S:24, 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:3, 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
|
PDB Export Chain Code C:CHAIN_CODE_1_LETTER, S:3, 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 |
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 |
3 Letter Code C:CODE_3_LETTER, S:9, 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 |
Code 1 Letter C:CODE_1_LETTER, S:15, A:1.0 | One code letter for the residue as specified in the PDB sequence and structure. |
C:CHEM_COMP_CODE, S:36, A:7.0 | 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 |
Residue PDB Code C:RESIDUE_PDB_CODE, S:9, A:3.0 | 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. |
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). |
PDB Insert Code C:PDB_INSERT_CODE, S:3, A:1.0 | The insertion code of the residue, as was originally found in the PDB. |
C:RESIDUE_SERIAL, S:5, 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. |
Entry Id C:ENTRY_ID, S:10, A:4.0 | The database identifier of the Entry |
C:ACCESSION_CODE, S:24, A:4.0 | The PDB accession code of the entry |
SwissProt accession C:SP_PRIMARY_ID, S:45, A:6.0 | The accession number (AC) associated with a swissprot entry (http://ca.expasy.org/sprot/userman.html#AC_line) |
Swissprot entry C:SP_SECONDARY_ID, S:765, A:9.0 | Swissprot entry name: The first item on the ID line is the entry name of the sequence. This name is a useful means of identifying a sequence (http://ca.expasy.org/sprot/userman.html#ID_line)
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SwissProt 1 Letter Code C:SP_1_LETTER_CODE, S:3, A:1.0 | This is the 1 letter code of the aminoacid as specified in the Swiss-prot database.
This can be different from the code in the PDB in very few cases where for several reasons the
protein sequence and the actual structure observed in the experiment deviate. |
Swissprot residue serial C:SP_SERIAL, S:10, A:3.0 | The serial identifier of the residue in the swiss-prot sequence.
This does not correspond to the PDB residue serial because often only partial fragments of the actual
sequence are involved and observed in the PDB experiment |
C:CATH_ID, S:18, A:6.0 | Cath Domain Names: MUST be SIX characters (e.g. 1cuk03).
CHARACTERS 1-4: PDB Code: The first 4 characters determine the PDB code e.g. 1cuk
CHARACTER 5: Chain Character: This determines which PDB chain is represented.A chain character of zero ('0') indicates that the PDB file has no chain field.
CHARACTER 6: Domain Number: A domain number of ZERO ('0') indicates that the domain is a whole PDB chain.
(http://www.biochem.ucl.ac.uk/bsm/cath/formats/CathList.html)
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CATH superfamily code C:CATHCODE, S:45, A:11.0 | CATH superfamily code that provide information about the CATH hierarchy.
(http://www.biochem.ucl.ac.uk/bsm/cath/cath_info.html)
The hierarchy is build up by the following levels
- Architecture, A-level: This describes the overall shape of the domain structure as determined by the orientations of the secondary structures but ignores the connectivity between the secondary structures.
- Topology (Fold family), T-level: Structures are grouped into fold families at this level depending on both the overall shape and connectivity of the secondary structures.
- Homologous Superfamily, H-level: This level groups together protein domains which are thought to share a common ancestor and can therefore be described as homologous.
- Sequence families, S-level: Structures within each H-level are further clustered on sequence identity.
(http://www.biochem.ucl.ac.uk/bsm/cath/formats/CathDomainDescriptionFile.html)
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Order In C:ORDER_IN, S:0, A:2.0 | The serial of the mapping to a cath domain when 2 different segments of the same chain map to the same CATH domain |
Begin residue C:BEG_RES, S:18, A:2.0 | The PDB seq of the first residue of the chain segment that belongs in the same mapping with this CATH domain |
End Residue C:END_RES, S:18, A:3.0 | The PDB seq of the last residue of the chain segment that belongs in the same mapping with this CATH domain |
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Reference attributes:Pfam Mapping Id - Naming attributes:Accession Code,Assembly Serial,Chain Code,Residue Serial,Ligand code,Pfam Id |
C:PFAM_MAPPING_ID, S:0, A:0.0 | Database identifier of the PFAM mapping |
C:ACCESSION_CODE, S:24, A:0.0 | The PDB accession code of the entry |
Entry Id C:ENTRY_ID, S:10, A:0.0 | The database identifier of the Entry |
Assembly Id C:ASSEMBLY_ID, S:10, A:0.0 | The database identifier of the Assembly |
C:ASSEMBLY_SERIAL, S:38, A:0.0 | The serial identifier of the assembly in the entry |
Residue Id C:RESIDUE_ID, S:0, A:0.0 | The database identifier of the Residue |
Ncbi Tax Id C:NCBI_TAX_ID, S:15, A:0.0 | The NCBI taxonomy identifier (taxid) that points to a node of the taxonomy tree |
Chain Id C:CHAIN_ID, S:10, A:0.0 | The database identifier of the Chain |
C:CHAIN_CODE, S:24, A:0.0 | 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) |
Chain Msd Code C:CHAIN_MSD_CODE, S:24, A:0.0 | 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:3, A:0.0 | 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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PDB Export Chain Code C:CHAIN_CODE_1_LETTER, S:3, A:0.0 | 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 |
Valid In Assymetric Unit C:NON_ASSEMBLY_VALID, S:1, A:0.0 | This item is to be used not only in an assembly context, but also to represent the original asymmetric unit |
3 Letter Code C:CODE_3_LETTER, S:9, A:0.0 | 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 |
Code 1 Letter C:CODE_1_LETTER, S:15, A:0.0 | One code letter for the residue as specified in the PDB sequence and structure. |
C:CHEM_COMP_CODE, S:36, A:0.0 | 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 |
Residue PDB Code C:RESIDUE_PDB_CODE, S:9, A:0.0 | 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. |
Residue PDB Seq C:RESIDUE_PDB_SEQ, S:4, A:0.0 | The sequence of the residue, as was originally found in the PDB (has to be used together with insert code). |
PDB Insert Code C:PDB_INSERT_CODE, S:3, A:0.0 | The insertion code of the residue, as was originally found in the PDB. |
C:RESIDUE_SERIAL, S:5, A:0.0 | 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. |
Chain C:CHAIN, S:3, A:0.0 | This field contains the chain identifier as in the original pfam data,
it should be the same as in the CHAIN_PDB_CODE , except in cases that,
this particular entry has been cleaned up |
Serial C:SERIAL, S:5, A:0.0 | (obsolete) same as the residue serial |
PDB 3 letter code C:PDB_ID, S:9, A:0.0 | This is the 3 letter code of the aminoacid as specified in the PDB
This can be different from the 3 letter code in the PDBe in very rare cases mainly when some cleanup was involved
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Pdb Seq C:PDB_SEQ, S:123, A:0.0 | The sequence of the residue, as was originally found in the PDB (has to be used together with insert code). |
SwissProt accession C:SP_PRIMARY, S:45, A:0.0 | The accession number (AC) associated with a swissprot entry (http://ca.expasy.org/sprot/userman.html#AC_line) |
SwissProt 1 Letter Code C:SP_COMPONENT, S:3, A:0.0 | This is the 1 letter code of the aminoacid as specified in the Swiss-prot database.
This can be different from the code in the PDB in very few cases where for several reasons the
protein sequence and the actual structure observed in the experiment deviate. |
Swissprot residue serial C:SP_SERIAL, S:10, A:0.0 | The serial identifier of the residue in the swiss-prot sequence.
This does not correspond to the PDB residue serial because often only partial fragments of the actual
sequence are involved and observed in the PDB experiment |
C:PFAM_ID, S:30, A:0.0 | The PFAM accession number
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Starting Residue C:SP_RES_FROM, S:5, A:0.0 | The Swissprot residue serial of the begining of the sequence segment maps to the same PFAM family |
Ending Residue C:SP_RES_TO, S:5, A:0.0 | The Swissprot residue serial of the end of the sequence segment maps to the same PFAM family |
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Reference attributes:Entry Id,Chain Code,SwissProt accession,Ending Residue,PFAM Id - Naming attributes:Accession Code,Chain Code,PFAM Id |
C:ACCESSION_CODE, S:8, A:4.0 | The PDB accession code of 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:PFAM_ID, S:10, A:7.0 | The database identifier of the Pfam |
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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C:ENTRY_ID, S:10, A:4.0 | The database identifier of the Entry |
Ending Residue  C:FROM_SP_SERIAL, S:5, A:3.0 | The Swissprot residue serial of the begining of the sequence segment maps to the Interpro IPR |
C:SP_PRIMARY_ID, S:15, A:6.0 | The accession number (AC) associated with a swissprot entry (http://ca.expasy.org/sprot/userman.html#AC_line) |
Swissprot entry C:SP_SECONDARY_ID, S:255, A:10.0 | Swissprot entry name: The first item on the ID line is the entry name of the sequence. This name is a useful means of identifying a sequence (http://ca.expasy.org/sprot/userman.html#ID_line)
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Starting Residue C:TO_SP_SERIAL, S:5, A:4.0 | The Swissprot residue serial of the begining of the sequence segment maps to the Interpro IPR |
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:Date, 
:Unknown
The attribute is a part of the name of an instance
The relation is the containment relation of the entity
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