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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1rn8
HYDROLASE HEADER
CRYSTAL STRUCTURE OF DUTPASE COMPLEXED WITH SUBSTRATE ANALOGUE IMIDO-DUTP TITLE
DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE; 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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MG G 999
32K ASP
71K ARG
119K GLN
MG B 999
32F ASP
71F ARG
119F GLN
MG L 999
32A ASP
71A ARG
119A GLN
MG V 999
32P ASP
71P ARG
119P GLN
MG A 999
32U ASP
71U ARG
119U GLN
MG Q 999
32Z ASP
71Z ARG
119Z GLN
DUP H 777
68A MET
71K ARG
72K SER
73K GLY
74K LEU
84A ASN
87A GLY
88A LEU
89A ILE
90A ASP
93A TYR
96A GLN
97A LEU
98A MET
100A SER
116K ARG
119K GLN
146F PHE
152F GLN
DUP C 777
68K MET
71F ARG
72F SER
73F GLY
74F LEU
84K ASN
87K GLY
88K LEU
89K ILE
90K ASP
93K TYR
96K GLN
97K LEU
98K MET
100K SER
116F ARG
119F GLN
146A PHE
152A GLN
DUP M 777
68F MET
71A ARG
72A SER
73A GLY
82F LEU
84F ASN
87F GLY
88F LEU
89F ILE
90F ASP
93F TYR
96F GLN
97F LEU
98F MET
100F SER
116A ARG
119A GLN
146K PHE
152K GLN
DUP W 777
68Z MET
71P ARG
72P SER
73P GLY
84Z ASN
87Z GLY
88Z LEU
89Z ILE
90Z ASP
93Z TYR
96Z GLN
97Z LEU
98Z MET
100Z SER
116P ARG
119P GLN
146U PHE
152U GLN
DUP B 777
68P MET
71U ARG
72U SER
73U GLY
74U LEU
84P ASN
87P GLY
88P LEU
89P ILE
90P ASP
93P TYR
96P GLN
97P LEU
98P MET
100P SER
116U ARG
119U GLN
146Z PHE
152Z GLN
DUP R 777
68U MET
71Z ARG
72Z SER
73Z GLY
74Z LEU
84U ASN
87U GLY
88U LEU
89U ILE
90U ASP
93U TYR
96U GLN
97U LEU
98U MET
100U SER
116Z ARG
119Z GLN
146P PHE
152P GLN
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
1dup Details
other holo-structures
pdb ID Ligand Unique ID
1seh UMPB_777 Details
UMPD_777
UMPF_777
1dud DUDB_153 Details
DUDF_153
DUDD_153
2hrm UC5H_777 Details
UC5E_777
UC5B_777
2hr6 DUDB_777 _MNG_997 Details
DUDJ_777 _MNC_997
DUDF_777 _MNK_997
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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DUP NAME: 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
FORMULA: C9 H16 N3 O13 P3
SMILES: OC1CC(OC1COP(O)(=O)NP(O)(=O)OP(O)(O)=O)N2C=CC(=O)NC2=O
MG NAME: MAGNESIUM ION
FORMULA: MG1
SMILES: [Mg++]
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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