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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1g4e
TRANSFERASE HEADER
THIAMIN PHOSPHATE SYNTHASE TITLE
THIAMIN PHOSPHATE SYNTHASE 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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29 TYR
31 ILE
57 GLN
59 ARG
61 LYS
92 ASN
93 ASP
107 HIS
109 GLY
110 GLN
111 GLU
112 ASP
130 ALA
147 TYR
149 GLY
151 GLY
152 PRO
156 THR
158 THR
159 LYS
162 THR
184 VAL
186 ILE
187 GLY
188 GLY
189 ILE
206 SER
207 MET
208 ILE
209 SER
210 ALA
1029 TYR
1031 ILE
1057 GLN
1059 ARG
1061 LYS
1092 ASN
1093 ASP
1107 HIS
1109 GLY
1110 GLN
1111 GLU
1112 ASP
1130 ALA
1132 HIS
1147 TYR
1149 GLY
1151 GLY
1152 PRO
1156 THR
1158 THR
1159 LYS
1162 THR
1184 VAL
1186 ILE
1187 GLY
1188 GLY
1189 ILE
1206 SER
1207 MET
1208 ILE
1209 SER
1210 ALA
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
1g6c IFPB2002 POPB2004 _MGB2008 TZPB2006 35 146 Details
IFPA2001 _MGA2007 POPA2003 TZPA2005 35 140
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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