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
holo-structureHelp

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

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1rxs
TRANSFERASE HEADER
E. COLI URIDINE PHOSPHORYLASE: 2'-DEOXYURIDINE PHOSPHATE COMPLEX TITLE
URIDINE PHOSPHORYLASE 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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PO4 B2011
1026B GLY
1030B ARG
1091B ARG
1092B ILE
1093B GLY
1094B THR
1196B GLU
2048b ARG
DUR C3032
1007C PHE
1008C HIS
1048C ARG
1076C ILE
2069c ILE
2091c ARG
2094c THR
2095c THR
2096c GLY
2162c PHE
2166c GLN
2168c ARG
2195c TYR
2196c GLU
2197c MET
2198c GLU
2220c ILE
2221c VAL
2223c ARG
2229c PRO
DUR c3032
1007C PHE
1008C HIS
1048C ARG
1076C ILE
2069c ILE
2091c ARG
2094c THR
2095c THR
2096c GLY
2162c PHE
2166c GLN
2168c ARG
2195c TYR
2196c GLU
2197c MET
2198c GLU
2220c ILE
2221c VAL
2223c ARG
2229c PRO
DUR B3022
1007B PHE
1008B HIS
1048B ARG
2069b ILE
2091b ARG
2094b THR
2095b THR
2096b GLY
2162b PHE
2166b GLN
2168b ARG
2195b TYR
2196b GLU
2197b MET
2198b GLU
2220b ILE
2221b VAL
2223b ARG
2229b PRO
DUR b3022
1007B PHE
1008B HIS
1048B ARG
2069b ILE
2091b ARG
2094b THR
2095b THR
2096b GLY
2162b PHE
2166b GLN
2168b ARG
2195b TYR
2196b GLU
2197b MET
2198b GLU
2220b ILE
2221b VAL
2223b ARG
2229b PRO
PO4 C2021
1026C GLY
1030C ARG
1091C ARG
1092C ILE
1093C GLY
1094C THR
1196C GLU
1198C GLU
2048c ARG
PO4 c3031
1048C ARG
2026c GLY
2027c ASP
2030c ARG
2091c ARG
2093c GLY
2094c THR
2198c GLU
PO4 C3031
1048C ARG
2026c GLY
2027c ASP
2030c ARG
2091c ARG
2093c GLY
2094c THR
2198c GLU
PO4 B3021
1048B ARG
2026b GLY
2030b ARG
2091b ARG
2092b ILE
2093b GLY
2094b THR
2198b GLU
DUR B2012
1069B ILE
1094B THR
1095B THR
1096B GLY
1162B PHE
1166B GLN
1168B ARG
1195B TYR
1196B GLU
1197B MET
1198B GLU
1220B ILE
1221B VAL
1223B ARG
1229B PRO
2007b PHE
2008b HIS
2048b ARG
2076b ILE
DUR C2022
1069C ILE
1094C THR
1095C THR
1096C GLY
1162C PHE
1166C GLN
1168C ARG
1195C TYR
1196C GLU
1197C MET
1198C GLU
1220C ILE
1221C VAL
1223C ARG
1229C PRO
2007c PHE
2008c HIS
2048c ARG
2076c ILE
V7O a5014
1125C PRO
2178a ARG
2179c HIS
PO4 A3011
2026a GLY
2027a ASP
2030a ARG
2091a ARG
2092a ILE
2093a GLY
2094a THR
3048A ARG
DUR A3012
2069a ILE
2091a ARG
2094a THR
2095a THR
2096a GLY
2162a PHE
2166a GLN
2168a ARG
2195a TYR
2196a GLU
2197a MET
2198a GLU
2220a ILE
2221a VAL
2223a ARG
2229a PRO
3007A PHE
3008A HIS
3048A ARG
3076A ILE
DUR a3012
2069a ILE
2091a ARG
2094a THR
2095a THR
2096a GLY
2162a PHE
2166a GLN
2168a ARG
2195a TYR
2196a GLU
2197a MET
2198a GLU
2220a ILE
2221a VAL
2223a ARG
2229a PRO
3007A PHE
3008A HIS
3048A ARG
3076A ILE
V7O b5013
2178c ARG
2179b HIS
V7O c5013
2178b ARG
2179a HIS
V7O c5014
2179a HIS
V7O b5014
2179b 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:

» PDB
» CSA
» PDBSum
» CATH
» Scop
» Pfam
» UniProt

LigPlot (hosted at the EBI):

» PO4 » Jmol
» DUR » Jmol
» V7O » Jmol
» V7O-V7O » Jmol
» K » Jmol
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 binding site (PDB)
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
1t0u Details
other holo-structures
pdb ID Ligand Unique ID
1rxu PO4E2061 THME2062 PO4F2061 Details
PO4C2041 PO4D2041 THMC2042
PO4A2011 THMA2012 PO4B2011 THMB2012
PO4E2051 PO4F2051 THME2052 THMF2052
PO4C2031 PO4D2031 THMC2032 THMD2032
PO4A2021 PO4B2021 THMA2022
1rxc R1PC2082 R1PD2082 URFC2081 URFD2081 Details
R1PE2032 URFF2031 URFE2031 R1PF2032
R1PE2002 URFE2001
R1PC2022 URFC2021
R1PA2012 URFA2011
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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DUR NAME: 2'-DEOXYURIDINE
FORMULA: C9 H12 N2 O5
SMILES: OCC1OC(CC1O)N2C=CC(=O)NC2=O
PO4 NAME: PHOSPHATE ION
FORMULA: O4 P1
SMILES: [O-]P([O-])([O-])=O
V7O NAME: META VANADATE
FORMULA: O19 V7
SMILES: O=[V](O[V](=O)(=O)O[V](=O)(=O)O([V](=O)=O)[V](=O)(=O)=O)O([V](=O)=O)[V](=O)(=O)=O
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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