university lille north of france LigASite database of binding sites
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LigASite v6.0 (nr25) - non-redundant
LigASite v6.0 (redundant) - redundant
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Browse dataset
apo-structureHelp

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

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1lx7
TRANSFERASE HEADER
STRUCTURE OF E. COLI URIDINE PHOSPHORYLASE AT 2.0A TITLE
URIDINE PHOSPHORYLASE 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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7 PHE
8 HIS
26 GLY
30 ARG
48 ARG
69 ILE
76 ILE
91 ARG
92 ILE
93 GLY
94 THR
95 THR
96 GLY
162 PHE
166 GLN
168 ARG
195 TYR
196 GLU
197 MET
198 GLU
220 ILE
221 VAL
223 ARG
229 PRO
1007 PHE
1008 HIS
1026 GLY
1030 ARG
1048 ARG
1069 ILE
1076 ILE
1091 ARG
1092 ILE
1093 GLY
1094 THR
1095 THR
1096 GLY
1125 PRO
1162 PHE
1166 GLN
1168 ARG
1195 TYR
1196 GLU
1197 MET
1198 GLU
1220 ILE
1221 VAL
1223 ARG
1229 PRO
2007 PHE
2008 HIS
2026 GLY
2027 ASP
2030 ARG
2048 ARG
2069 ILE
2076 ILE
2091 ARG
2092 ILE
2093 GLY
2094 THR
2095 THR
2096 GLY
2162 PHE
2166 GLN
2168 ARG
2178 ARG
2179 HIS
2195 TYR
2196 GLU
2197 MET
2198 GLU
2220 ILE
2221 VAL
2223 ARG
2229 PRO
3007 PHE
3008 HIS
3048 ARG
3076 ILE
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:

» PDB
» CSA
» PDBSum
» CATH
» Scop
» Pfam
» UniProt
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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» XML File
» XML Schema
» Coordinates (PDB)
» apo binding site (PDB)
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
1rxu PO4E2061 THME2062 PO4F2061 22 92 Details
PO4C2041 PO4D2041 THMC2042 22 91
PO4A2011 THMA2012 PO4B2011 THMB2012 22 85
PO4E2051 PO4F2051 THME2052 THMF2052 22 90
PO4C2031 PO4D2031 THMC2032 THMD2032 22 82
PO4A2021 PO4B2021 THMA2022 22 89
1rxc R1PC2082 R1PD2082 URFC2081 URFD2081 23 97 Details
R1PE2032 URFF2031 URFE2031 R1PF2032 23 85
R1PE2002 URFE2001 23 84
R1PC2022 URFC2021 23 88
R1PA2012 URFA2011 23 83
1rxs DURB2012 PO4B2011 21 93 Details
DURA3012 DURa3012 PO4A3011 21 90
DURC2022 PO4C2021 21 91
V7Oa5014 V7Oc5014 V7Ob5013 V7Ob5014 V7Oc5013 22 70
DURC3032 PO4c3031 PO4C3031 DURc3032 21 87
DURB3022 PO4B3021 DURb3022 21 82
v6.0
October 2008		 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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