university lille north of france LigASite database of binding sites
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LigASite v9.7 (nr25) - non-redundant
LigASite v9.7 (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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1rxc
TRANSFERASE HEADER
E. COLI URIDINE PHOSPHORYLASE: 5-FLUOROURACIL RIBOSE-1- 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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R1P L2082
7N PHE
8N HIS
26K GLY
30K ARG
48N ARG
69K ILE
76N ILE
91K ARG
92K ILE
93K GLY
94K THR
162K PHE
196K GLU
197K MET
198K GLU
URF P2081
7N PHE
94K THR
95K THR
96K GLY
162K PHE
166K GLN
168K ARG
195K TYR
196K GLU
197K MET
220K ILE
221K VAL
223K ARG
229K PRO
R1P F2032
7H PHE
8H HIS
26E GLY
30E ARG
48H ARG
69E ILE
76H ILE
91E ARG
93E GLY
94E THR
162E PHE
196E GLU
197E MET
198E GLU
URF J2031
7H PHE
94E THR
95E THR
96E GLY
162E PHE
166E GLN
168E ARG
195E TYR
196E GLU
197E MET
220E ILE
221E VAL
223E ARG
229E PRO
R1P D2012
7A PHE
8A HIS
26C GLY
30C ARG
48A ARG
69C ILE
91C ARG
93C GLY
94C THR
162C PHE
196C GLU
197C MET
198C GLU
220C ILE
URF B2011
7A PHE
94C THR
95C THR
96C GLY
162C PHE
166C GLN
168C ARG
195C TYR
196C GLU
197C MET
220C ILE
221C VAL
223C ARG
229C PRO
R1P I2002
7E PHE
8E HIS
26H GLY
30H ARG
48E ARG
69H ILE
76E ILE
91H ARG
93H GLY
94H THR
162H PHE
196H GLU
197H MET
198H GLU
220H ILE
R1P O2022
7K PHE
8K HIS
26N GLY
30N ARG
48K ARG
69N ILE
91N ARG
93N GLY
94N THR
162N PHE
196N GLU
197N MET
198N GLU
URF M2021
7K PHE
94N THR
95N THR
96N GLY
162N PHE
166N GLN
168N ARG
195N TYR
196N GLU
197N MET
220N ILE
221N VAL
223N ARG
229N PRO
URF G2001
94H THR
95H THR
96H GLY
162H PHE
166H GLN
168H ARG
195H TYR
196H GLU
197H MET
220H ILE
221H VAL
223H ARG
229H PRO
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):

no entry
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 PO4K2101 THML2102 Details
PO4Q2121 THMR2122
PO4N2111 THMO2112
PO4H2091 THMI2092
PO4E2081 THMF2082
PO4B2071 THMC2072
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
1rxs DURG2102 PO4F2101 Details
DURC3112 PO4B3111
DURQ2112 PO4N2111
DURL2122 PO4I2121
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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R1P NAME: RIBOSE-1-PHOSPHATE
FORMULA: C5 H11 O8 P1
SMILES: OCC1OC(OP(O)(O)=O)C(O)C1O
URF NAME: 5-FLUOROURACIL
FORMULA: C4 H3 N2 O2 F1
SMILES: FC1=CNC(=O)NC1=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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