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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26 GLY
30 ARG
48 ARG
68 GLY
69 ILE
76 ILE
91 ARG
92 ILE
93 GLY
94 THR
95 THR
96 GLY
162 PHE
166 GLN
168 ARG
195 TYR
196 GLU
197 MET
198 GLU
220 ILE
221 VAL
223 ARG
229 PRO
1007 PHE
1008 HIS
1026 GLY
1030 ARG
1048 ARG
1068 GLY
1069 ILE
1076 ILE
1091 ARG
1092 ILE
1093 GLY
1094 THR
1095 THR
1096 GLY
1162 PHE
1166 GLN
1168 ARG
1195 TYR
1196 GLU
1197 MET
1198 GLU
1220 ILE
1221 VAL
1223 ARG
1229 PRO
2026 GLY
2027 ASP
2030 ARG
2069 ILE
2091 ARG
2092 ILE
2093 GLY
2094 THR
2095 THR
2096 GLY
2162 PHE
2166 GLN
2168 ARG
2195 TYR
2196 GLU
2197 MET
2198 GLU
2220 ILE
2221 VAL
2223 ARG
2229 PRO
3007 PHE
3008 HIS
3048 ARG
3076 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
1rxu PO4K2101 THML2102 22 89 Details
PO4Q2121 THMR2122 22 86
PO4N2111 THMO2112 22 94
PO4H2091 THMI2092 22 95
PO4E2081 THMF2082 22 91
PO4B2071 THMC2072 22 96
1rxc R1PL2082 URFP2081 23 97 Details
R1PF2032 URFJ2031 23 85
R1PD2012 URFB2011 23 83
R1PI2002 URFG2001 23 84
R1PO2022 URFM2021 23 88
3kvv R2BW_256 URFX_254 SO4V_255 23 94 Details
R2BS_256 URFT_254 SO4R_255 23 89
R2BG_256 URFH_254 SO4F_255 23 90
R2BC_256 SO4B_255 URFD_254 23 88
R2BO_256 SO4N_255 URFP_254 23 92
R2BK_256 URFL_254 SO4J_255 23 90
1rxs DURG2102 PO4F2101 21 94 Details
DURC3112 PO4B3111 21 82
DURQ2112 PO4N2111 21 96
DURL2122 PO4I2121 21 92
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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