university lille north of france LigASite database of binding sites
apo-structureHelp

PDB ID and HEADER, TITLE and COMPND records of the PDB file.

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7icd
OXIDOREDUCTASE (NAD(A)-CHOH(D)) HEADER
REGULATION OF AN ENZYME BY PHOSPHORYLATION AT THE ACTIVE SITE TITLE
ISOCITRATE DEHYDROGENASE COMPND
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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16 LEU
19 GLY
21 LEU
37 ILE
41 VAL
96 ARG
97 VAL
100 LYS
102 PRO
103 LEU
104 THR
105 THR
113 GLU
115 ASN
116 VAL
119 ARG
126 ILE
128 LEU
129 ARG
152 PHE
153 ARG
160 TYR
212 ALA
216 TYR
230 LYS
232 ASN
233 ILE
281 ILE
283 ASP
284 ALA
287 GLN
288 GLN
291 LEU
292 ARG
307 ASP
311 ASP
320 ILE
321 GLY
328 ILE
329 GLY
330 ASP
331 GLU
332 CYS
333 ALA
335 PHE
336 GLU
337 ALA
338 THR
339 HIS
340 GLY
341 THR
342 ALA
343 PRO
344 LYS
345 TYR
351 VAL
352 ASN
362 MET
366 HIS
391 TYR
392 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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holo-structuresHelp

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
1hj6 GOLE1417 GOLF1418 12 70 Details
IPMJ1419 NAPH1420 _MGI1421 61 210
IPMD1419 NAPB1420 _MGC1421 61 213
GOLK1417 GOLL1418 12 74
v9.7
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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