university lille north of france LigASite database of binding sites
apo-structureHelp

PDB ID and HEADER, TITLE and COMPND records of the PDB file.

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1bbc
CARBOXYLIC ESTER HYDROLASE HEADER
STRUCTURE OF RECOMBINANT HUMAN RHEUMATOID ARTHRITIC SYNOVIAL FLUID PHOSPHOLIPASE A2 AT 2.2 ANGSTROMS RESOLUTION TITLE
PHOSPHOLIPASE A2 COMPND
Illustration of Binding SiteHelp

Figure highlighting the binding site residues. Figures were drawn with Molscript (7) and rendered with Raster3D (8). PISA coordinates (3) are used when available (all entries except NMR).

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Contacting ResiduesHelp

List of binding site residues detected in this protein.

Column 1 gives the position, coloured on a yellow-to-red scale depending on the fraction of corresponding holo-structures where the residue is in contact with a ligand.
Column 2 gives the 3-letter amino acid code, coloured according to physico-chemical type.

Chain ID's of residues are not mentioned in this page because all chains in the apo-structure refer to the same protein.

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2 LEU
3 VAL
5 PHE
6 HIS
9 ILE
17 ALA
18 ALA
19 LEU
21 TYR
22 GLY
23 PHE
27 HIS
28 CYS
29 GLY
30 VAL
31 GLY
33 ARG
44 CYS
47 HIS
48 ASP
49 CYS
51 TYR
52 LYS
55 GLU
56 LYS
62 LYS
94 ALA
98 PHE
111 TYR
113 SER
115 LYS
External LinksHelp

PDB The Protein Data Bank
CSA Catalytic Site Atlas
PDBSum Overview of the macromolecular structure
CATH Protein Structure Classification
Scop Structural Classification of Proteins
Pfam Protein Families and Domains
UniProt Universal Protein Resource

LIGPLOT (only on holo-pages) is hosted at the EBI.

The LigPlot Jmol links point directly to the Jmol visualisation interface provided on the PDBSum page.

Note that due to different software used, the atomic contacts of LigPlot and LigASite do not necessarily correspond.

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Links to external databases:

Download FilesHelp

Several files are provided for download:

• The XML file defining the residue-ligand contacts; this file contains data on the apo and all holo-structures.
• The XML Schema file defining the semantics of the XML file
• 3D coordinates of the structure used in constructing LigASite (PISA structure file whenever available, PDB file otherwise.
• 3D coordinates of the combined binding residues in the apo structure
• 3D coordinates of the binding residues of the holo structure (only on the holo page)

Coordinate files are in PDB format.

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holo-structuresHelp

Table describing the holo-structures and ligands used to define the binding sites.

Column 1 gives the PDB ID of the holo-structure.
Column 2 gives the unique ID of the ligand; a space-separated list of HET-groups that constitute the ligand (see Methods). Each HET-group in the ligand is uniquely identified by a string in which the first four characters are the three-letter HET ID from the PDB file followed by the chain ID from the PISA file, and the last four characters are the residue sequence number from the PDB file.
Column 3 gives the number of atoms in each ligand.
Column 4 gives the number of protein-ligand inter-atomic contacts.

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pdb ID Ligand Unique ID #atoms #contacts
1poe GELB_935 _CAB_802 32 133 Details
GELA_930 _CAA_801 32 138
1db5 6IND_200 _CAC_198 29 129 Details
6INH_200 _CAG_198 29 129
1j1a _CAG_201 BHPH2301 37 141 Details
BHPD1301 _CAG_201 BHPH2301 _CAC_201 74 276
1kqu BR4D_501 _CAC_301 30 119 Details
BR4H_501 _CAG_301 30 122
1kvo OAPC_190 _CAC_191 37 134 Details
OAPD_190 _CAD_191 37 131
OAPB_190 _CAB_191 37 123
OAPA_190 _CAA_191 37 129
OAPF_190 _CAF_191 37 136
OAPE_190 _CAE_191 37 128
1dcy I3NH1201 _CAG_198 24 120 Details
I3ND1201 _CAC_198 24 123
1ayp INBB_202 _CAB_303 36 160 Details
INBD_204 _CAD_307 36 151
INBC_203 _CAC_305 36 153
INBE_205 _CAE_309 36 155
INBF_206 _CAF_311 36 158
INBA_201 _CAA_301 36 147
1db4 8IND_200 _CAC_198 30 129 Details
8INH_200 _CAG_198 30 134
v9.7
April 2012
Interdisciplinary Research Institute, Computational Biology, Villeneuve d'Ascq, France
University College London, Biomolecular Structure and Modelling Unit, London, UK
Hospital for Sick Children and University of Toronto, Structural Biology and Biochemistry Program, Toronto, Canada
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