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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2hrm
HYDROLASE HEADER
CRYSTAL STRUCTURE OF DUTPASE COMPLEXED WITH SUBSTRATE ANALOGUE METHYLENE-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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UC5 H 777
32G ASP
68A MET
71G ARG
72G SER
73G GLY
82A LEU
84A ASN
87A GLY
88A LEU
89A ILE
90A ASP
93A TYR
96A GLN
97A LEU
98A MET
99A ILE
100A SER
UC5 E 777
32D ASP
68G MET
71D ARG
72D SER
73D GLY
82G LEU
84G ASN
87G GLY
88G LEU
89G ILE
90G ASP
93G TYR
96G GLN
97G LEU
98G MET
100G SER
UC5 B 777
32A ASP
68D MET
71A ARG
72A SER
73A GLY
82D LEU
84D ASN
87D GLY
88D LEU
89D ILE
90D ASP
93D TYR
96D GLN
97D LEU
98D MET
100D SER
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
1rn8 DUPH_777 _MGG_999 Details
DUPC_777 _MGB_999
DUPM_777 _MGL_999
DUPW_777 _MGV_999
DUPB_777 _MGA_999
DUPR_777 _MGQ_999
1seh UMPB_777 Details
UMPD_777
UMPF_777
1dud DUDB_153 Details
DUDF_153
DUDD_153
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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UC5 NAME: not_found
FORMULA: not_found
SMILES: not_found
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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