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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45 VAL
46 GLY
47 ARG
48 GLY
49 LYS
50 TYR
51 SER
53 VAL
66 ILE
68 LYS
81 GLU
85 LEU
95 VAL
113 PHE
114 GLU
115 TYR
116 VAL
117 ASN
118 ASN
120 ASP
156 ASP
158 LYS
160 HIS
161 ASN
163 MET
174 ILE
175 ASP
176 TRP
177 GLY
178 LEU
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
2oxy K17B1002 13 76 Details
K17A1001 13 73
1om1 IQAA_338 22 99 Details
1zoe DMSA_701 K25A_501 _CLA_601 21 106 Details
1lp4 ANPA_340 _MGA_342 _MGA_341 33 126 Details
1zoh K44A_501 _NAA_601 18 88 Details
3fl5 TXQA_338 20 96 Details
2qc6 G12A___1 15 78 Details
3pzh EMOA___1 20 96 Details
1f0q EMOA_400 20 87 Details
2oxd K32A_338 14 75 Details
3pwd CZ0A___1 20 94 Details
2oxx K22A_501 14 75 Details
1ds5 AMPD_801 23 92 Details
1zog K37A_501 15 76 Details
1j91 TBSA_338 13 71 Details
TBSB_338 13 75
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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