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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1mqe
HYDROLASE HEADER
STRUCTURE OF THE MT-ADPRASE IN COMPLEX WITH GADOLIDIUM AND ADP-RIBOSE, A NUDIX ENZYME TITLE
ADPR 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 B 208
18A ALA
19A ILE
20A PHE
36D THR
37D ARG
38D GLU
39D VAL
42A HIS
45A ALA
62A GLN
64A ARG
66A THR
76A ALA
77A GLY
78A LEU
80A ASP
93A GLU
113A THR
114D ALA
115D PRO
116D GLY
117D PHE
120A GLU
166A ASN
168A ILE
APR E 208
18D ALA
19D ILE
20D PHE
36A THR
37A ARG
38A GLU
39A VAL
42D HIS
45D ALA
62D GLN
64D ARG
66D THR
76D ALA
77D GLY
78D LEU
80D ASP
93D GLU
113D THR
114A ALA
115A PRO
116A GLY
117A PHE
120D GLU
166D ASN
168D ILE
GD3 F 301
93D GLU
96D GLU
97D GLU
GD3 C 301
93A GLU
96A GLU
97A 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
1mp2 Details
other holo-structures
pdb ID Ligand Unique ID
1mqw ADVG_301 _MNH_403 _MNI_402 _MNJ_401 Details
ADVB_301 _MNE_401 _MND_402 _MNC_403
1mk1 APRD_208 Details
APRB_208
1mr2 A12B_301 _MNC_401 Details
A12E_301 _MNF_401
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
GD3 NAME: GADOLINIUM ION
FORMULA: GD1
SMILES: [Gd+3]
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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