PDBe database documentation

Entities of Active sites

The entities that belong to a specific mart
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

Active sites Information about the active sites of the macromolecule, and the way that ligands and drugs bind to a protein. The site information is provided in a uniform and consistent way, since it is calculated internally in PDBe (http://www.ebi.ac.uk/msd-srv/msdsite/index.jsp). The active sites of a protein chain are determined based on the contacts of the chain with a ligand. There are many ways that contacts are defined based on different types of bonds and interactions, that take into account the distance and angles of the atoms, as well as other characteristics of the ligands and residues like planes. An active site can be defined not only for a particular atom, but also for a plane of a molecule.
Angle A:15, R:8, T:ANGLE, I:594000	Contains values of angles and distances for ligand as metal ineraction
Angle between planes A:10, R:6, T:ANGLE2PLANE, I:92000
Contact A:12, R:6, T:CONTACT, I:4720000
Contact Type A:5, R:0, T:CONTACT_TYPE, I:6
Neighbour Type A:2, R:5, T:NEIGHBOUR_TYPE, I:0
Plane Center A:18, R:7, T:PLANE_CENTER, I:2810000	Contains data about geometrical plane centres in a structure, data into this table is loaded by placeCenter C++ program by Adel Golovin
Residue Contact A:21, R:10, T:RESIDUE_CONTACT, I:715000
Residue Geometry A:4, R:1, T:RESIDUE_GEOMETRY, I:7280
Site A:17, R:14, T:SITE, I:3870000	Presents interacting site of a chemical compound, could be two types : ATOM and PLANE see SITE_TYPE table. The interaction that is presented here is always between bound molecule or modified residue and macromolecule chain.
Site Type A:2, R:1, T:SITE_TYPE, I:2	Type of interacting site - reference table, possible values: ATOM, PLANE

Attributes/Relations of Active sites Entities

The attributes and relations that belong to a specific entity
Attribute Details: Type of the attribute String

:String,

:Integer,

:Number,

:Date,

:Unknown
C=Name of the database column
S=Maximum size of the attribute
=Actual average size used for the attribute
Naming

The attribute is a part of the name of an instance

The attribute is a part of the reference key of an instance
Hidden

The attribute is not supposed to be visible and used for queries
Summery

The attribute is supposed to be used in summary reports (lists) for the entity

Relation Details: Cardinality of the relation

:Optional, Many

:Many

=Reverse relation of the entity that the relation refers to

=Entity that this relation establishes an association (reverse entity)

The relation is the containment relation of the entity

The relation is associated with an external entity from a different mart
Hidden

The relation is not supposed to be visible and used for queries

Angle Contains values of angles and distances for ligand as metal ineraction Reference attributes:Id - Naming attributes:Id
Id C:ID, S:0, A:4.0	The identifier of Angle
Angle C:ANGLE, S:27, A:3.0
Assembly Id C:ASSEMBLY_ID, S:0, A:4.0	The database identifier of the Assembly
Assembly Serial C:ASSEMBLY_SERIAL, S:0, A:2.0	The serial identifier of the assembly in the entry
Contact Type Id1 C:CONTACT_TYPE_ID1, S:0, A:2.0
Contact Type Id2 C:CONTACT_TYPE_ID2, S:0, A:2.0
Distance1 C:DISTANCE1, S:27, A:3.0
Distance2 C:DISTANCE2, S:27, A:3.0
Entry Id C:ENTRY_ID, S:0, A:4.0	The database identifier of the Entry
Ligand Site Id C:LIGAND_SITE_ID, S:0, A:5.0	The database identifier of the Ligand Site
Model Id C:MODEL_ID, S:0, A:4.0	The database identifier of the Model
Neighbour Site Id1 C:NEIGHBOUR_SITE_ID1, S:0, A:5.0
Neighbour Site Id2 C:NEIGHBOUR_SITE_ID2, S:0, A:5.0
Neighbour Type Id1 C:NEIGHBOUR_TYPE_ID1, S:0, A:2.0
Neighbour Type Id2 C:NEIGHBOUR_TYPE_ID2, S:0, A:2.0
of related	Reverse relation:has of Reverse entity:Assembly - Relation attributes:Assembly Id
of related	Reverse relation:has of Reverse entity:Entry - Relation attributes:Entry Id
of related	Reverse relation:has of Reverse entity:Model - Relation attributes:Model Id
1st related	Reverse relation:1st of of Reverse entity:Neighbour Type - Relation attributes:Neighbour Type Id1
2nd related	Reverse relation:2nd of of Reverse entity:Site - Relation attributes:Neighbour Site Id1
1st related	Reverse relation:1st of of Reverse entity:Site - Relation attributes:Ligand Site Id
2nd related	Reverse relation:2nd of of Reverse entity:Neighbour Type - Relation attributes:Neighbour Type Id2
3rd related	Reverse relation:3rd of of Reverse entity:Site - Relation attributes:Neighbour Site Id2

Angle between planes Reference attributes:Id - Naming attributes:Id
Id C:ID, S:0, A:4.0	The identifier of Angle to Plane
Angle C:ANGLE, S:27, A:2.0	The angle between the normals of the plane
Assembly Id C:ASSEMBLY_ID, S:0, A:4.0	The database identifier of the Assembly
Assembly Serial C:ASSEMBLY_SERIAL, S:0, A:2.0	The serial identifier of the assembly in the entry
Distance C:DISTANCE, S:27, A:3.0	The distance between the centers of the plane
Entry Id C:ENTRY_ID, S:0, A:4.0	The database identifier of the Entry
Ligand Site Id C:LIGAND_SITE_ID, S:0, A:5.0	The database identifier of the Ligand Site
Model Id C:MODEL_ID, S:0, A:4.0	The database identifier of the Model
Neighbour Site Id C:NEIGHBOUR_SITE_ID, S:0, A:5.0	The database identifier of the Neighbour Site
Neighbour Type Id C:NEIGHBOUR_TYPE_ID, S:0, A:2.0	The database identifier of the Neighbour Type
of related	Reverse relation:has of Reverse entity:Assembly - Relation attributes:Assembly Id
of related	Reverse relation:has of Reverse entity:Model - Relation attributes:Model Id
of related	Reverse relation:has of Reverse entity:Entry - Relation attributes:Entry Id
1st related	Reverse relation:1st of of Reverse entity:Site - Relation attributes:Ligand Site Id
has related	Reverse relation:of of Reverse entity:Neighbour Type - Relation attributes:Neighbour Type Id
2nd related	Reverse relation:2nd of of Reverse entity:Site - Relation attributes:Neighbour Site Id

Contact Reference attributes:Id - Naming attributes:Id
Id C:ID, S:0, A:5.0	The identifier of Contact
Assembly Id C:ASSEMBLY_ID, S:0, A:4.0	The database identifier of the Assembly
Assembly Serial C:ASSEMBLY_SERIAL, S:0, A:2.0	The serial identifier of the assembly in the entry
Distance C:DISTANCE, S:27, A:3.0	The distance between atoms
Entry Id C:ENTRY_ID, S:0, A:4.0	The database identifier of the Entry
Ligand Acceptor Donor C:LIGAND_ASSEPTOR_DONOR, S:1, A:1.0	Indicates whether ligand's atom is donor or acceptor in case of hydrogen bond
Ligand Site Id C:LIGAND_SITE_ID, S:0, A:5.0	The database identifier of the Ligand Site
Model Id C:MODEL_ID, S:0, A:4.0	The database identifier of the Model
Neighbour Acceptor Donor C:NEIGHBOUR_ASSEPTOR_DONOR, S:1, A:1.0	Indicates whether interacting residue's atom is donor or acceptor in case of hydrogen bond
Neighbour Site Id C:NEIGHBOUR_SITE_ID, S:0, A:5.0	The database identifier of the Neighbour Site
Neighbour Type Id C:NEIGHBOUR_TYPE_ID, S:0, A:2.0	The database identifier of the Neighbour Type
Type Id C:TYPE_ID, S:0, A:2.0	The database identifier of the Type
of related	Reverse relation:has of Reverse entity:Assembly - Relation attributes:Assembly Id
of related	Reverse relation:has of Reverse entity:Model - Relation attributes:Model Id
of related	Reverse relation:has of Reverse entity:Entry - Relation attributes:Entry Id
2nd related	Reverse relation:2nd of of Reverse entity:Site - Relation attributes:Neighbour Site Id
1st related	Reverse relation:1st of of Reverse entity:Site - Relation attributes:Ligand Site Id
has related	Reverse relation:of of Reverse entity:Neighbour Type - Relation attributes:Neighbour Type Id

Contact Type Reference attributes:id - Naming attributes:name
id C:ID, S:0, A:2.0
bond Strength C:BOND_STRENGTH, S:0, A:2.0
name C:NAME, S:30, A:8.0
method C:METHOD, S:80, A:9.0
method Reliability C:METHOD_RELIABILITY, S:0, A:2.0

Neighbour Type Reference attributes:Id - Naming attributes:Name
Id C:ID, S:0, A:0.0
Name C:NAME, S:30, A:0.0
1st of related	Reverse relation:1st of Reverse entity:Angle - Relation attributes:Id
2nd of related	Reverse relation:2nd of Reverse entity:Angle - Relation attributes:Id
of related	Reverse relation:has of Reverse entity:Contact - Relation attributes:Id
of related	Reverse relation:has of Reverse entity:Angle between planes - Relation attributes:Id
of related	Reverse relation:has of Reverse entity:Residue Contact - Relation attributes:Id

Plane Center Contains data about geometrical plane centres in a structure, data into this table is loaded by placeCenter C++ program by Adel Golovin Reference attributes:Id - Naming attributes:Id
Id C:ID, S:0, A:5.0	The identifier of the plane center
Alt Id C:ALT_ID, S:0, A:2.0	The database identifier of the alternative location of the plane atoms
Assembly Id C:ASSEMBLY_ID, S:0, A:4.0	The database identifier of the Assembly
Assembly Serial C:ASSEMBLY_SERIAL, S:0, A:2.0	The serial identifier of the assembly in the entry
ALT Code C:ATL_CODE, S:8, A:1.0	The Code of alternative location of the plane atoms
Atoms Name C:ATOMS_NAME, S:256, A:26.0	A comma separated list of the atoms of the plane
Chain Id C:CHAIN_ID, S:0, A:5.0	The database identifier of the Chain
Entry Id C:ENTRY_ID, S:0, A:4.0	The database identifier of the Entry
Model Id C:MODEL_ID, S:0, A:4.0	The database identifier of the Model
Normal X C:NX, S:27, A:4.0	The X value of the normal to the plane
Normal Y C:NY, S:27, A:4.0	The Y value of the normal to the plane
Normal Z C:NZ, S:27, A:4.0	The Z value of the normal to the plane
Occupancy C:OCCUPANCY, S:27, A:2.0	Occupancy of the plane center
Plane Id C:PLANE_ID, S:0, A:4.0	The database identifier of the Plane reference to small compounds database CHEM_PLANE
Residue Id C:RESIDUE_ID, S:0, A:5.0	The database identifier of the Residue
X C:X, S:27, A:5.0	The X coordinate of the plane center
Y C:Y, S:27, A:5.0	The Y coordinate of the plane center
Z C:Z, S:27, A:5.0	The Z coordinate of the plane center
of related	Reverse relation:has of Reverse entity:Assembly - Relation attributes:Assembly Id
of related	Reverse relation:has of Reverse entity:Model - Relation attributes:Model Id
of related	Reverse relation:has of Reverse entity:Residue - Relation attributes:Residue Id
of related	Reverse relation:has of Reverse entity:Alt - Relation attributes:Alt Id
has related	Reverse relation:of of Reverse entity:Site - Relation attributes:Id
of related	Reverse relation:has of Reverse entity:Chain - Relation attributes:Chain Id
of related	Reverse relation:has of Reverse entity:Entry - Relation attributes:Entry Id

Residue Contact Reference attributes:Residue Contact Id - Naming attributes:Residue Contact Id
Assembly Id C:ASSEMBLY_ID, S:0, A:4.0	The database identifier of the Assembly
Bond Strength C:BOND_STRENGTH, S:0, A:2.0
Contacts Count C:CONTACTS_COUNT, S:0, A:2.0
Entry Id C:ENTRY_ID, S:0, A:4.0	The database identifier of the Entry
Ligand Code 3Letter C:LIGAND_CODE_3_LETTER, S:3, A:3.0
Ligand Geometry Id C:LIGAND_GEOMETRY_ID, S:0, A:2.0	The database identifier of the Ligand Geometry
Ligand Id C:LIGAND_ID, S:0, A:5.0	The database identifier of the Ligand (DEIC_ID)
Ligand Residue Id C:LIGAND_RESIDUE_ID, S:0, A:5.0	The database identifier of the Ligand Residue
Macromol Sec Struct Type C:MACROMOL_SEC_STRUCT_TYPE, S:0, A:2.0
Model Id C:MODEL_ID, S:0, A:4.0	The database identifier of the Model
Neighbour Code 3Letter C:NEIGHBOUR_CODE_3_LETTER, S:3, A:3.0
Neighbour Id C:NEIGHBOUR_ID, S:0, A:5.0	The database identifier of the interacting residue (DEIC_ID)
Helix Id C:HELIX_ID, S:0, A:3.0
Neighbour Main Atom Data Id C:NEIGHBOUR_MAIN_ATOM_DATA_ID, S:0, A:1.0	The database identifier of the Neighbour Main Atom Data
Sheet Id C:SHEET_ID, S:0, A:2.0
Neighbour Residue Id C:NEIGHBOUR_RESIDUE_ID, S:0, A:5.0	The database identifier of the Neighbour Residue
Sheet Type C:SHEET_TYPE, S:2, A:1.0
Neighbour Type Id C:NEIGHBOUR_TYPE_ID, S:0, A:2.0	The database identifier of the Neighbour Type
Turn Id C:TURN_ID, S:0, A:2.0
Residue Contact Id C:RESIDUE_CONTACT_ID, S:0, A:4.0	The database identifier of the Residue Contact
Interaction Type Id C:INTERACTION_TYPE_ID, S:0, A:2.0
involved related	Reverse relation:contacts of Reverse entity:Sheet - Relation attributes:Sheet Id
neighbour related	Reverse relation:neighbour of Reverse entity:Residue - Relation attributes:Neighbour Residue Id
of related	Reverse relation:has of Reverse entity:Model - Relation attributes:Model Id
of related	Reverse relation:has of Reverse entity:Entry - Relation attributes:Entry Id
has related	Reverse relation:of of Reverse entity:Neighbour Type - Relation attributes:Neighbour Type Id
involved related	Reverse relation:contacts of Reverse entity:Helix - Relation attributes:Helix Id
ligand related	Reverse relation:ligand of Reverse entity:Residue - Relation attributes:Ligand Residue Id
main neighbour related	Reverse relation:main neighbour of of Reverse entity:Atom Data - Relation attributes:Neighbour Main Atom Data Id
of related	Reverse relation:has of Reverse entity:Assembly - Relation attributes:Assembly Id
involved related	Reverse relation:contacts of Reverse entity:Turn - Relation attributes:Turn Id

Residue Geometry Reference attributes:Residue Id - Naming attributes:Geometry Name
Residue Id C:RESIDUE_ID, S:0, A:5.0	The database identifier of the Residue
Geometry Id C:GEOMETRY_ID, S:0, A:2.0	The database identifier of the Geometry
Geometry Name C:GEOMETRY_NAME, S:30, A:11.0
Entry Id C:ENTRY_ID, S:10, A:4.0	The database identifier of the Entry
of related	Reverse relation:has of Reverse entity:Residue - Relation attributes:Residue Id

Site Presents interacting site of a chemical compound, could be two types : ATOM and PLANE see SITE_TYPE table. The interaction that is presented here is always between bound molecule or modified residue and macromolecule chain. Reference attributes:Id - Naming attributes:Id
Id C:ID, S:0, A:5.0	The site identifier
Atom Data Id C:ATOM_DATA_ID, S:0, A:6.0	The database identifier of the Atom Data
Atom Id C:ATOM_ID, S:0, A:5.0	The database identifier of the Atom
Atom Name C:ATOM_NAME, S:12, A:4.0
Chain Id C:CHAIN_ID, S:0, 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
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:0, A:4.0	The database identifier of the Entry
Geometry Id C:GEOMETRY_ID, S:0, A:2.0	The database identifier of the Geometry
Number of Contacts C:NUM_CONTACTS, S:0, A:1.0
Ordering C:ORDERING, S:0, A:3.0
PDB SEQ C:PDB_SEQ, S:0, A:3.0	The sequence of the residue, as was originally found in the PDB (has to be used together with insert code).
Plane Center Id C:PLANE_CENTER_ID, S:0, A:2.0	The database identifier of the Plane Center
Residue Id C:RESIDUE_ID, S:0, A:5.0	The database identifier of the Residue
Symbol C:SYMBOL, S:2, A:2.0	The chemical element of the site in case when site is atom (not plane)
Type Id C:TYPE_ID, S:0, A:2.0	The database identifier of the Type referes to: ATOM or PLANE
Substruct Code C:SUBSTRUCT_CODE, S:5, A:2.0
of related	Reverse relation:has of Reverse entity:Atom Data - Relation attributes:Atom Data Id
1st of related	Reverse relation:1st of Reverse entity:Angle - Relation attributes:Id
3rd of related	Reverse relation:3rd of Reverse entity:Angle - Relation attributes:Id
2nd of related	Reverse relation:2nd of Reverse entity:Contact - Relation attributes:Id
1st of related	Reverse relation:1st of Reverse entity:Contact - Relation attributes:Id
2nd of related	Reverse relation:2nd of Reverse entity:Angle between planes - Relation attributes:Id
1st of related	Reverse relation:1st of Reverse entity:Angle between planes - Relation attributes:Id
2nd of related	Reverse relation:2nd of Reverse entity:Angle - Relation attributes:Id
type related	Reverse relation:of of Reverse entity:Site Type - Relation attributes:Type Id
of related	Reverse relation:has of Reverse entity:Atom - Relation attributes:Atom Id
of related	Reverse relation:has of Reverse entity:Chain - Relation attributes:Chain Id
of related	Reverse relation:has of Reverse entity:Entry - Relation attributes:Entry Id
of related	Reverse relation:has of Reverse entity:Residue - Relation attributes:Residue Id
of related	Reverse relation:has of Reverse entity:Plane Center - Relation attributes:Plane Center Id

Site Type Type of interacting site - reference table, possible values: ATOM, PLANE Reference attributes:Id - Naming attributes:Name
Id C:ID, S:0, A:2.0
Name C:NAME, S:30, A:5.0	The name of interacting site type, possible values: ATOM, PLANE
of related	Reverse relation:type of Reverse entity:Site - Relation attributes:Id