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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1v8r
HYDROLASE HEADER
CRYSTAL STRUCTURE ANALYSIS OF THE ADP-RIBOSE PYROPHOSPHATASE COMPLEXED WITH ADP-RIBOSE AND ZN TITLE
ADP-RIBOSE PYROPHOSPHATASE 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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APR D 619
18A ARG
19A ILE
27E ARG
28E TYR
29E GLU
30E ILE
33A HIS
36A ALA
37A VAL
52A GLN
54A ARG
55A PRO
56A ALA
63A GLU
66A ALA
67A GLY
68A LEU
70A GLU
81A ARG
82A GLU
86A GLU
102E SER
103E PRO
104E GLY
105E PHE
108A GLU
110A THR
155A THR
APR H 619
18E ARG
19E ILE
27A ARG
28A TYR
29A GLU
30A ILE
33E HIS
36E ALA
37E VAL
52E GLN
54E ARG
55E PRO
56E ALA
63E GLU
66E ALA
67E GLY
68E LEU
70E GLU
81E ARG
82E GLU
86E GLU
102A SER
103A PRO
104A GLY
105A PHE
108E GLU
110E THR
155E THR
ZN B 301
81A ARG
82A GLU
85A GLU
86A GLU
ZN F 301
81E ARG
82E GLU
85E GLU
86E GLU
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
1v8i Details
other holo-structures
pdb ID Ligand Unique ID
1v8l APRD_619 Details
APRB_619
1v8s AMPC_619 _MGB_301 Details
AMPF_619 _MGE_301
1v8m APRF_619 _GDG_300 _GDH_301 Details
APRB_619 _GDD_301 _GDC_300
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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APR NAME: ADENOSINE-5-DIPHOSPHORIBOSE
FORMULA: C15 H23 N5 O14 P2
SMILES: Nc1ncnc2[n](cnc12)C3OC(COP(O)(=O)OP(O)(=O)OCC4OC(O)C(O)C4O)C(O)C3O
ZN NAME: ZINC ION
FORMULA: ZN1
SMILES: [Zn++]
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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