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

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

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2iea
OXIDOREDUCTASE HEADER
E. COLI PYRUVATE DEHYDROGENASE TITLE
PYRUVATE DEHYDROGENASE E1 COMPONENT COMPND
Illustration of Binding SiteHelp

Figure showing the binding site residues. Ligands are displayed as CPK. Figures were drawn with Molscript (7) and rendered with Raster3D (8). PISA coordinates (3) are used when available (all entries except NMR). Ligands do not appear on the picture when PISA fails to apply symmetry operations to ligand coordinates.

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HETgroup - Residue ContactsHelp

List of binding site residues detected in this holo-structure.

Column 1 gives the position, coloured on a yellow-to-red scale depending on the number of holo-structures where the residue is in contact with a ligand.
Column 2 gives the identifier of the chain to which the residue belongs.
Column 3 gives the 3-letter amino acid code, coloured according to physico-chemical type.

The binding residues in this holo structure are listed for each ligand independently, following the ligand's unique ID.

Note that since PISA files are used whenever available, chain identifiers may differ from those in original PDB files.

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TDP B 887
106A HIS
109A SER
140A GLN
142A HIS
177A TYR
192A VAL
193A SER
194A MET
229A GLY
230A ASP
231A GLY
232A GLU
235A GLU
258A ASN
260A ASN
262A GLN
263A ARG
264A LEU
392A LYS
520D ALA
521D ASP
522D GLU
569D ILE
571D GLU
599D TYR
602D PHE
606D ARG
640D HIS
TDP E 887
106D HIS
109D SER
140D GLN
142D HIS
177D TYR
192D VAL
193D SER
194D MET
229D GLY
230D ASP
231D GLY
232D GLU
235D GLU
258D ASN
260D ASN
262D GLN
263D ARG
264D LEU
392D LYS
520A ALA
521A ASP
522A GLU
569A ILE
571A GLU
599A TYR
602A PHE
606A ARG
640A HIS
MG C 888
230A ASP
258A ASN
260A ASN
262A GLN
MG F 888
230D ASP
258D ASN
260D ASN
262D GLN
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:

LigPlot (hosted at the EBI):

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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Hide table of related structures
Help

List of related structure, containing both the apo-structure and other holo-structures.

Column 1 gives the PDB ID and column 2 the unique ID of the ligands (holo-structures only).

Clicking the blue 'Hide table of related structures' button removes the entire table.

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apo-structure
pdb ID
2g67 Details
other holo-structures
pdb ID Ligand Unique ID
1rp7 TZDB_889 _MGC_890 Details
TZDE_887 _MGF_888
1l8a TDPB_887 _MGC_888 Details
TDPE_887 _MGF_888
2g28 TDKB_887 _MGC_888 Details
TDKE_887 _MGF_888
2g25 TDKB_887 _MGD_888 Details
TDKH_887 _MGJ_888
Ligand ListHelp

Ligands present in this holo structure.

Column 1 shows the ligand HET code
Column 2 shows the name, chemical formula and (non-stereo) SMILES string.

Data in column 2 appears as 'not_found' when it is not present in the file 'pdb2smiles.xml' from www.rcsb.org.

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TDP NAME: THIAMIN DIPHOSPHATE
FORMULA: C12 H18 N4 O7 P2 S1
SMILES: Cc1ncc(C[n+]2csc(CCOP(O)(=O)OP(O)([O-])=O)c2C)c(N)n1
MG NAME: MAGNESIUM ION
FORMULA: MG1
SMILES: [Mg++]
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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