university lille north of france LigASite database of binding sites
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LigASite v9.7 (nr25) - non-redundant
LigASite v9.7 (redundant) - redundant
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Browse dataset
holo-structureHelp

PDB ID and HEADER, TITLE and COMPND records of the PDB file.

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3c2f
TRANSFERASE HEADER
CRYSTAL STRUCTURE OF THE QUINOLINATE PHOSPHORIBOSYL TRANSFERASE (BNA6) FROM SACCHAROMYCES CEREVISIAE COMPLEXED WITH PRPP TITLE
NICOTINATE-NUCLEOTIDE PYROPHOSPHORYLASE 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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PRP J 300
48K LYS
106K GLU
107K ARG
110K LEU
142I THR
144I LYS
165I HIS
174I MET
176I LYS
206I GLU
225I MET
254I GLU
256I SER
257I GLY
258I GLY
276I SER
277I THR
278I SER
282I GLN
288K ASP
289K PHE
290K SER
292K LYS
PRP F 300
48G LYS
106G GLU
107G ARG
110G LEU
141E GLY
142E THR
144E LYS
165E HIS
174E MET
176E LYS
206E GLU
225E MET
254E GLU
256E SER
257E GLY
258E GLY
276E SER
277E THR
278E SER
282E GLN
288G ASP
289G PHE
290G SER
292G LYS
PRP H 300
48E LYS
106E GLU
107E ARG
110E LEU
142G THR
144G LYS
165G HIS
174G MET
176G LYS
206G GLU
225G MET
254G GLU
256G SER
257G GLY
258G GLY
276G SER
277G THR
278G SER
282G GLN
288E ASP
289E PHE
290E SER
292E LYS
PRP D 300
48A LYS
106A GLU
107A ARG
110A LEU
142C THR
144C LYS
165C HIS
174C MET
176C LYS
206C GLU
225C MET
254C GLU
256C SER
257C GLY
258C GLY
276C SER
277C THR
278C SER
282C GLN
288A ASP
289A PHE
290A SER
292A LYS
PRP L 300
48I LYS
106I GLU
107I ARG
110I LEU
141K GLY
142K THR
144K LYS
165K HIS
174K MET
176K LYS
206K GLU
225K MET
254K GLU
256K SER
257K GLY
258K GLY
276K SER
277K THR
278K SER
282K GLN
288I ASP
289I PHE
290I SER
292I LYS
PRP B 300
48C LYS
106C GLU
107C ARG
110C LEU
142A THR
144A LYS
165A HIS
174A MET
176A LYS
206A GLU
225A MET
254A GLU
256A SER
257A GLY
258A GLY
276A SER
277A THR
278A SER
282A GLN
288C ASP
289C PHE
290C SER
292C LYS
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:

» PDB
» CSA
» PDBSum
» CATH
» Scop
» Pfam
» UniProt

LigPlot (hosted at the EBI):

no entry
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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» XML File
» XML Schema
» Coordinates (PDB)
» apo binding site (PDB)
» holo binding site (PDB)
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
3c2e Details
other holo-structures
pdb ID Ligand Unique ID
3c2v PHTO_301 PRPQ_300 Details
PHTR_301 PRPN_300
PHTC_301 PRPE_300
PHTI_301 PRPK_300
PHTL_301 PRPH_300
PHTF_301 PRPB_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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PRP NAME: ALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC ACID
FORMULA: C5 H13 O14 P3
SMILES: OC1C(O)C(OC1COP(O)(O)=O)OP(O)(=O)OP(O)(O)=O
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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