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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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 N2111
1026M GLY
1030M ARG
1091M ARG
1093M GLY
1094M THR
1196M GLU
3048R ARG
DUR G2102
1007H PHE
1008H HIS
1048H ARG
1068E GLY
1069E ILE
1076H ILE
1094E THR
1095E THR
1096E GLY
1162E PHE
1166E GLN
1168E ARG
1195E TYR
1196E GLU
1197E MET
1198E GLU
1220E ILE
1221E VAL
1223E ARG
1229E PRO
DUR L2122
1007E PHE
1008E HIS
1048E ARG
1069H ILE
1076E ILE
1094H THR
1095H THR
1096H GLY
1162H PHE
1166H GLN
1168H ARG
1195H TYR
1196H GLU
1197H MET
1198H GLU
1220H ILE
1221H VAL
1223H ARG
1229H PRO
PO4 F2101
1026E GLY
1030E ARG
1048H ARG
1091E ARG
1092E ILE
1093E GLY
1094E THR
1196E GLU
PO4 I2121
1026H GLY
1030H ARG
1048E ARG
1091H ARG
1093H GLY
1094H THR
1196H GLU
DUR Q2112
1069M ILE
1094M THR
1095M THR
1096M GLY
1162M PHE
1166M GLN
1168M ARG
1195M TYR
1196M GLU
1197M MET
1198M GLU
1220M ILE
1221M VAL
1223M ARG
1229M PRO
3007R PHE
3008R HIS
3048R ARG
3076R ILE
PO4 B3111
2026A GLY
2027A ASP
2030A ARG
2091A ARG
2092A ILE
2093A GLY
2094A THR
2198A GLU
3048D ARG
DUR C3112
2069A ILE
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
3007D PHE
3008D HIS
3048D ARG
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
1t0u Details
other holo-structures
pdb ID Ligand Unique ID
1rxu PO4K2101 THML2102 Details
PO4Q2121 THMR2122
PO4N2111 THMO2112
PO4H2091 THMI2092
PO4E2081 THMF2082
PO4B2071 THMC2072
1rxc R1PL2082 URFP2081 Details
R1PF2032 URFJ2031
R1PD2012 URFB2011
R1PI2002 URFG2001
R1PO2022 URFM2021
3kvv R2BW_256 URFX_254 SO4V_255 Details
R2BS_256 URFT_254 SO4R_255
R2BG_256 URFH_254 SO4F_255
R2BC_256 SO4B_255 URFD_254
R2BO_256 SO4N_255 URFP_254
R2BK_256 URFL_254 SO4J_255
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
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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