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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17 THR
18 VAL
19 PRO
22 GLU
66 ASN
99 THR
100 ASP
102 ARG
103 LEU
137 GLN
163 GLU
165 TYR
186 TYR
187 GLY
188 GLY
189 SER
191 ARG
195 ARG
213 PHE
214 GLY
215 ASN
237 LYS
238 ILE
240 MET
243 VAL
256 ILE
261 TYR
265 PHE
267 THR
268 LEU
269 ARG
272 GLU
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
1j39 UPGA_400 36 145 Details
1c3j UDPA_353 25 103 Details
1jiu UDPA_353 _MGA_354 26 124 Details
1m5r TRSE_501 UDPB_401 33 145 Details
1jix UDPA_500 _CAA_600 26 107 Details
1jg7 UDPA_400 _MNA_401 26 122 Details
2bgu UDPA_353 25 99 Details
1ixy UDPB_401 _MGD_501 26 119 Details
1nvk UDPA_700 _MNA_701 26 113 Details
1qkj UDPA_353 25 117 Details
1jg6 UDPA_400 25 111 Details
1jiv UDPA_353 _MGA_354 26 118 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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