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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3ef5
HYDROLASE HEADER
STRUCTURE OF THE RNA PYROPHOSPHOHYDROLASE BDRPPH IN COMPLEX WITH DGTP TITLE
PROBABLE PYROPHOSPHOHYDROLASE 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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DGT A3800
22A ILE
24A VAL
25A VAL
26A ALA
40A ARG
45A SER
46A LEU
51A GLU
52A PHE
54A GLY
55A GLY
56A LYS
70A GLU
74A GLU
92A TYR
97A ILE
99A ILE
101A PHE
115A HIS
133A PRO
135A ALA
136A ASN
DGT B3801
22B ILE
24B VAL
25B VAL
26B ALA
40B ARG
51B GLU
52B PHE
54B GLY
55B GLY
56B LYS
70B GLU
74B GLU
92B TYR
97B ILE
99B ILE
101B PHE
133B PRO
135B ALA
136B ASN
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
3ees Details
other holo-structures
pdb ID Ligand Unique ID
3ffu GTPE4033 _MGB_156 _MGD_155 _MGC_154 Details
GTPJ4032 _MGH_154 _MGG_156 _MGI_155
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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DGT NAME: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
FORMULA: C10 H16 N5 O13 P3
SMILES: NC1=Nc2[n](cnc2C(=O)N1)C3CC(O)C(COP(O)(=O)OP(O)(=O)OP(O)(O)=O)O3
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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