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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2yxf
IMMUNE SYSTEM HEADER
THE HIGH RESOLUTION CRYSTAL STRUCTURE OF BETA2- MICROGLOBULIN UNDER PHYSIOLOGICAL CONDITIONS TITLE
BETA-2-MICROGLOBULIN 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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6 LYS
8 GLN
9 VAL
10 TYR
11 SER
12 ARG
13 HIS
14 PRO
15 ALA
26 TYR
28 SER
29 GLY
56 PHE
57 SER
58 LYS
59 ASP
60 TRP
61 SER
63 TYR
95 TRP
96 ASP
97 ARG
99 MET
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
2x4r GOLE1103 GOLH1102 12 71 Details
2x4o GOLB1276 MESE1100 18 78 Details
GOLI1279 MESO1100 MESC1277 30 109
1i4f 1PGE_502 17 76 Details
1PGB_501 17 83
2x4p GOLC1276 MESD1101 18 70 Details
GOLB1100 GOLC1276 MESD1101 24 108
1tvb GOLH1003 GOLJ1017 GOLK1020 18 87 Details
3o3b GOLD_276 GOLF_278 12 79 Details
1gzp TWTC1282 GM2B1280 74 327 Details
D12D1281 TWTC1282 GM2B1280 86 391
1zt4 AGHB_282 60 297 Details
2x70 GOLD1277 MESE1100 16 79 Details
GOLB1276 GOLD1277 MESE1100 22 108
1gzq NO3G1283 PIIB1280 TWTC1285 82 371 Details
D12D1284 PIIB1280 TWTC1285 90 424
2x4u GOLG1276 GOLH1279 MESI1100 24 103 Details
GOLB1278 GOLH1279 MESI1100 24 104
MESC1277 MESP1100 24 85
3hcv CIRD___5 CIRE___6 22 95 Details
3d18 MESH_102 TRSG_279 20 84 Details
2x4t GOLB1277 MESC1099 18 70 Details
1uqs GMMB1283 74 403 Details
3dtx CIRD___5 CIRE___6 22 104 Details
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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