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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1gta
GLUTATHIONE TRANSFERASE HEADER
CRYSTAL STRUCTURES OF A SCHISTOSOMAL DRUG AND VACCINE TARGET: GLUTATHIONE S-TRANSFERASE FROM SCHISTOSOMA JAPONICA AND ITS COMPLEX WITH THE LEADING ANTISCHISTOSOMAL DRUG PRAZIQUANTEL TITLE
GLUTATHIONE S-TRANSFERASE 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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6 TYR
7 TRP
8 TRP
9 ILE
10 ILE
11 GLY
12 LEU
13 LEU
40 TRP
41 ARG
42 ARG
44 LYS
45 LYS
52 PRO
53 ASN
54 LEU
55 PRO
56 PRO
66 GLN
67 SER
68 MET
69 MET
96 GLY
97 GLY
99 LEU
100 ASP
101 ASP
103 TYR
104 TYR
107 SER
108 ARG
110 TYR
111 TYR
204 GLN
205 GLY
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
1ua5 GTTC1002 20 89 Details
GTTF1002 20 88
1m9b IBGB_220 28 124 Details
IBGD_220 28 122
1m9a GTXD_220 26 123 Details
GTXB_220 26 119
1m99 GTSB_220 23 92 Details
GTSD_220 23 89
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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