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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1r15
HYDROLASE HEADER
APLYSIA ADP RIBOSYL CYCLASE WITH BOUND NICOTINAMIDE AND R5P TITLE
ADP-RIBOSYL CYCLASE 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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N B1179
75A MET
76A PHE
77A TRP
78A SER
79A GLY
97A LEU
98A GLU
140A TRP
144A SER
147A TYR
170A ARG
173A SER
174A PHE
175A PHE
179A GLU
N F1179
75E MET
76E PHE
77E TRP
78E SER
79E GLY
97E LEU
98E GLU
140E TRP
144E SER
147E TYR
170E ARG
173E SER
174E PHE
175E PHE
179E GLU
NCA C 319
77A TRP
81A TYR
98A GLU
106A LEU
107A ASN
108A SER
109A LEU
140A TRP
174A PHE
NCA G 329
77E TRP
81E TYR
98E GLU
107E ASN
108E SER
128E PHE
140E TRP
174E PHE
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
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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
1r12 Details
other holo-structures
pdb ID Ligand Unique ID
3i9j NFDA_301 Details
AVVB_301 NCAC_302
3i9o AVWA_301 Details
AVWB_301
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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NCA NAME: NICOTINAMIDE
FORMULA: C6 H6 N2 O1
SMILES: NC(=O)c1cccnc1
N NAME: ANY 5'-MONOPHOSPHATE NUCLEOTIDE
FORMULA: C5 H11 O7 P1
SMILES: OC1COC(COP(O)(O)=O)C1O
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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