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 THR
32 ASP
33 PHE
37 ASP
38 PHE
40 GLY
42 ARG
47 ARG
49 HIS
51 SER
52 ARG
53 THR
54 GLU
59 ALA
60 ASP
61 ASN
62 THR
63 SER
65 TRP
67 GLU
86 TYR
87 ALA
89 THR
95 THR
100 SER
101 PRO
102 ALA
105 GLU
107 ALA
109 ARG
113 GLY
115 CYS
117 HIS
119 THR
120 ALA
212 THR
232 ASP
233 PHE
234 GLY
235 ASP
237 ASP
238 PHE
247 ARG
249 HIS
251 SER
252 ARG
253 THR
254 GLU
259 ALA
260 ASP
261 ASN
262 THR
263 SER
265 TRP
267 GLU
286 TYR
287 ALA
289 THR
295 THR
300 SER
301 PRO
302 ALA
305 GLU
307 ALA
309 ARG
313 GLY
315 CYS
317 HIS
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
1jif BLMF_402 _CUE_404 _CLB_502 95 196 Details
BLMH_401 _CUG_403 _CLD_501 95 185
1jie BLMC_402 96 218 Details
BLMD_401 96 201
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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