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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12 SER
14 VAL
19 VAL
20 GLY
40 SER
41 VAL
43 PHE
45 ASN
46 HIS
47 THR
48 GLY
52 TRP
56 VAL
84 TYR
85 THR
86 ARG
113 ASP
115 VAL
118 ASP
119 GLN
120 ARG
127 TYR
148 THR
149 PRO
150 ASN
153 GLU
186 THR
187 SER
199 LEU
201 ALA
223 MET
224 HIS
225 LYS
226 VAL
228 ALA
230 PHE
231 VAL
232 GLY
233 THR
234 GLY
235 ASP
237 PHE
260 VAL
263 MET
264 HIS
267 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
1yhj R6CD_313 26 127 Details
R6CB_313 26 124
1ygj RMCD1001 27 113 Details
RMCB1001 27 110
1rfu ADPD2402 _ZNB2403 PLPC2401 43 185 Details
ADPH7402 PLPG7401 _ZNF7403 43 178
1rft ACPH_401 _ZNG_403 __KI_404 33 139 Details
ACPC_401 _ZNB_403 __KD_404 33 137
1ygk RRCD1001 26 124 Details
RRCB1001 26 120
1rfv ADPF1401 _ZNE1402 28 118 Details
ADPC_401 _ZNB_402 28 122
1lhr ATPG_402 _ZNF_404 __KH_406 33 143 Details
ATPC_401 _ZNB_403 __KD_405 33 131
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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