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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3c2v
TRANSFERASE HEADER
CRYSTAL STRUCTURE OF THE QUINOLINATE PHOSPHORIBOSYL TRANSFERASE (BNA6) FROM SACCHAROMYCES CEREVISIAE COMPLEXED WITH PRPP AND THE INHIBITOR PHTHALATE 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 H 300
48G LYS
106G GLU
107G ARG
110G LEU
142J THR
144J LYS
176J LYS
206J GLU
225J MET
227J ASP
256J SER
257J GLY
258J GLY
259J LEU
276J SER
277J THR
278J SER
279J SER
282J GLN
288G ASP
289G PHE
290G SER
291G LEU
292G LYS
PRP B 300
48A LYS
106A GLU
107A ARG
110A LEU
142D THR
144D LYS
176D LYS
206D GLU
225D MET
227D ASP
256D SER
257D GLY
258D GLY
259D LEU
276D SER
277D THR
278D SER
282D GLN
288A ASP
289A PHE
290A SER
291A LEU
292A LYS
PRP Q 300
48P LYS
106P GLU
107P ARG
110P LEU
142M THR
144M LYS
176M LYS
206M GLU
225M MET
227M ASP
256M SER
257M GLY
258M GLY
259M LEU
276M SER
277M THR
278M SER
282M GLN
288P ASP
289P PHE
290P SER
291P LEU
292P LYS
PRP N 300
48M LYS
106M GLU
107M ARG
110M LEU
142P THR
144P LYS
176P LYS
206P GLU
225P MET
227P ASP
256P SER
257P GLY
258P GLY
259P LEU
276P SER
277P THR
278P SER
282P GLN
288M ASP
289M PHE
290M SER
291M LEU
292M LYS
PRP E 300
48D LYS
106D GLU
107D ARG
110D LEU
142A THR
144A LYS
176A LYS
206A GLU
225A MET
227A ASP
256A SER
257A GLY
258A GLY
259A LEU
276A SER
277A THR
278A SER
279A SER
282A GLN
288D ASP
289D PHE
290D SER
291D LEU
292D LYS
PRP K 300
48J LYS
106J GLU
107J ARG
110J LEU
142G THR
144G LYS
176G LYS
206G GLU
225G MET
227G ASP
256G SER
257G GLY
258G GLY
259G LEU
276G SER
277G THR
278G SER
282G GLN
288J ASP
289J PHE
290J SER
291J LEU
292J LYS
PHT O 301
107P ARG
142M THR
143M ARG
144M LYS
165M HIS
166M ARG
174M MET
176M LYS
225M MET
254M GLU
256M SER
276M SER
PHT R 301
107M ARG
142P THR
143P ARG
144P LYS
165P HIS
166P ARG
174P MET
176P LYS
225P MET
254P GLU
256P SER
276P SER
PHT C 301
107D ARG
142A THR
143A ARG
144A LYS
165A HIS
166A ARG
174A MET
176A LYS
225A MET
254A GLU
256A SER
276A SER
PHT I 301
107J ARG
141G GLY
142G THR
143G ARG
144G LYS
165G HIS
166G ARG
174G MET
176G LYS
225G MET
254G GLU
256G SER
276G SER
PHT L 301
107G ARG
142J THR
143J ARG
144J LYS
165J HIS
166J ARG
174J MET
176J LYS
225J MET
254J GLU
256J SER
276J SER
PHT F 301
107A ARG
141D GLY
142D THR
143D ARG
144D LYS
165D HIS
166D ARG
174D MET
176D LYS
225D MET
254D GLU
256D SER
276D SER
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
3c2e Details
other holo-structures
pdb ID Ligand Unique ID
3c2f PRPJ_300 Details
PRPF_300
PRPH_300
PRPD_300
PRPL_300
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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PHT NAME: PHTHALIC ACID
FORMULA: C8 H6 O4
SMILES: OC(=O)c1ccccc1C(O)=O
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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