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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38 ASP
40 THR
41 PRO
46 ASP
67 GLU
68 GLU
82 ASP
83 PRO
84 LEU
85 ASP
86 GLY
87 THR
88 PHE
155 TYR
156 TYR
164 LYS
165 ARG
167 ARG
170 GLY
171 SER
172 ALA
175 GLU
189 ASP
191 ARG
195 MET
196 LEU
197 ARG
200 ASP
338 ASP
340 THR
341 PRO
346 ASP
367 GLU
368 GLU
382 ASP
383 PRO
384 LEU
385 ASP
386 GLY
387 THR
388 PHE
455 TYR
456 TYR
464 LYS
465 ARG
467 ARG
470 GLY
471 SER
472 ALA
489 ASP
491 ARG
495 MET
496 LEU
499 TYR
500 ASP
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
1lby F6PD_595 PO4H_593 _MNK_590 _MNI_592 _MNJ_591 24 101 Details
F6PL_295 _MNC_292 _MNE_291 PO4B_293 _MNF_290 24 103
1lbx IPDD_295 _CAB_291 _CAC_290 18 83 Details
IPDH_595 _CAG_591 _CAF_590 18 80
1lbz FBPJ_595 _CAI_590 _CAH_591 22 91 Details
FBPE_295 _CAD_290 _CAC_291 22 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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