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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2g67
OXIDOREDUCTASE HEADER
E. COLI PYRUVATE DEHYDROGENASE E1 COMPONENT (APOENZYME) TITLE
PYRUVATE DEHYDROGENASE E1 COMPONENT 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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106 HIS
109 SER
140 GLN
142 HIS
177 TYR
192 VAL
193 SER
194 MET
229 GLY
230 ASP
231 GLY
232 GLU
235 GLU
258 ASN
260 ASN
262 GLN
263 ARG
264 LEU
392 LYS
407 HIS
408 GLN
410 LYS
520 ALA
521 ASP
522 GLU
525 THR
569 ILE
571 GLU
599 TYR
602 PHE
606 ARG
633 LEU
636 GLU
640 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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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
2iea TDPB_887 _MGC_888 27 130 Details
TDPE_887 _MGF_888 27 129
1rp7 TZDB_889 _MGC_890 28 132 Details
TZDE_887 _MGF_888 28 135
1l8a TDPB_887 _MGC_888 27 125 Details
TDPE_887 _MGF_888 27 123
2g28 TDKB_887 _MGC_888 35 144 Details
TDKE_887 _MGF_888 35 138
2g25 TDKB_887 _MGD_888 35 144 Details
TDKH_887 _MGJ_888 35 138
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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