university lille north of france LigASite database of binding sites

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

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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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10 ILE
11 ASP
12 ASP
13 ALA
15 ASP
16 ALA
30 ASP
32 ASP
33 ASP
34 GLY
35 SER
37 GLY
38 SER
39 SER
40 ASP
42 TRP
73 ILE
74 SER
75 TYR
76 GLY
77 ASP
78 SER
79 SER
80 GLY
81 ASP
83 SER
110 SER
111 PHE
114 ASP
115 SER
116 PHE
117 ILE
119 ASP
120 LEU
122 ILE
125 LEU
128 LEU
130 THR
133 LEU
135 THR
189 PHE
194 PHE
213 ILE
215 ASP
217 GLY
218 THR
219 THR
220 LEU
221 GLY
222 TYR
223 THR
224 LEU
226 TYR
248 VAL
249 GLY
275 PHE
280 PHE
282 PRO
283 ILE
284 PHE
291 PHE
296 GLY
297 ILE
299 ILE
300 ILE
301 ILE
302 ILE
304 ILE
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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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
1epp DCIE_333 STAE_332 MTFE_334 LYSE_331 PHEE_330 MASE_329 47 233 Details
2v00 ACTA1335 V15A1336 GOLA1332 26 119 Details
ACTA1334 V15A1336 GOLA1332 26 126
3q6y DMSA4001 S47A5001 37 98 Details
3prs 1PEA2001 RITA1001 DMSA5001 70 250 Details
3pww ROCA1001 49 160 Details
3pb5 F63A1001 15 81 Details
4er1 BNAB___1 25 84 Details
1e82 HFAB___2 SMCB___3 PCHC___4 MRMB___1 46 172 Details
3psy PG4A4001 RB9A1001 50 172 Details
DMSA2001 PG4A4001 RB9A1001 54 189
1eed BOCD___4 FOGC___3 CHSB___1 36 141 Details
3pgi F41A2001 19 97 Details
3pm4 F5NA2001 19 85 Details
3pi0 DMSA4001 F91A2001 22 104 Details
3pmu F7LA2001 18 83 Details
3pmy 41LA2001 19 89 Details
1od1 DPHB_401 TSMB_400 18 71 Details
3pbz DMSA4001 F02A1001 19 99 Details
1e81 CPYC___4 SMCB___3 HFAB___2 MRMB___1 46 166 Details
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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