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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1rxu
TRANSFERASE HEADER
E. COLI URIDINE PHOSPHORYLASE: THYMIDINE 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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THM L2102
7G PHE
8G HIS
48G ARG
69J ILE
76G ILE
94J THR
95J THR
96J GLY
162J PHE
166J GLN
168J ARG
195J TYR
196J GLU
197J MET
198J GLU
220J ILE
221J VAL
223J ARG
229J PRO
THM R2122
7M PHE
8M HIS
48M ARG
68P GLY
69P ILE
76M ILE
94P THR
95P THR
96P GLY
162P PHE
166P GLN
168P ARG
195P TYR
196P GLU
197P MET
198P GLU
220P ILE
221P VAL
223P ARG
229P PRO
THM O2112
7P PHE
8P HIS
48P ARG
69M ILE
76P ILE
94M THR
95M THR
96M GLY
162M PHE
166M GLN
168M ARG
195M TYR
196M GLU
197M MET
198M GLU
220M ILE
221M VAL
223M ARG
229M PRO
THM I2092
7J PHE
8J HIS
48J ARG
69G ILE
76J ILE
91G ARG
94G THR
95G THR
96G GLY
162G PHE
166G GLN
168G ARG
195G TYR
196G GLU
197G MET
198G GLU
220G ILE
221G VAL
223G ARG
229G PRO
THM F2082
7A PHE
8A HIS
48A ARG
69D ILE
94D THR
95D THR
96D GLY
162D PHE
166D GLN
168D ARG
195D TYR
196D GLU
197D MET
198D GLU
220D ILE
221D VAL
223D ARG
229D PRO
THM C2072
7D PHE
8D HIS
48D ARG
69A ILE
76D ILE
94A THR
95A THR
96A GLY
162A PHE
166A GLN
168A ARG
195A TYR
196A GLU
197A MET
198A GLU
220A ILE
221A VAL
223A ARG
229A PRO
PO4 K2101
26J GLY
30J ARG
48G ARG
69J ILE
91J ARG
92J ILE
93J GLY
94J THR
198J GLU
PO4 Q2121
26P GLY
30P ARG
48M ARG
91P ARG
92P ILE
93P GLY
94P THR
PO4 N2111
26M GLY
30M ARG
48P ARG
91M ARG
92M ILE
93M GLY
94M THR
PO4 H2091
26G GLY
30G ARG
48J ARG
91G ARG
93G GLY
94G THR
PO4 E2081
26D GLY
30D ARG
48A ARG
91D ARG
92D ILE
93D GLY
94D THR
PO4 B2071
26A GLY
30A ARG
48D ARG
68A GLY
69A ILE
91A ARG
92A ILE
93A GLY
94A THR
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
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
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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PO4 NAME: PHOSPHATE ION
FORMULA: O4 P1
SMILES: [O-]P([O-])([O-])=O
THM NAME: THYMIDINE
FORMULA: C10 H14 N2 O5
SMILES: CC1=CN(C2CC(O)C(CO)O2)C(=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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