university lille north of france LigASite database of binding sites
apo-structureHelp

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

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3c2e
TRANSFERASE HEADER
CRYSTAL STRUCTURE AT 1.9A OF THE APO QUINOLINATE PHOSPHORIBOSYL TRANSFERASE (BNA6) FROM SACCHAROMYCES CEREVISIAE TITLE
NICOTINATE-NUCLEOTIDE PYROPHOSPHORYLASE COMPND
Illustration of Binding SiteHelp

Figure highlighting the binding site residues. Figures were drawn with Molscript (7) and rendered with Raster3D (8). PISA coordinates (3) are used when available (all entries except NMR).

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Contacting ResiduesHelp

List of binding site residues detected in this protein.

Column 1 gives the position, coloured on a yellow-to-red scale depending on the fraction of corresponding holo-structures where the residue is in contact with a ligand.
Column 2 gives the 3-letter amino acid code, coloured according to physico-chemical type.

Chain ID's of residues are not mentioned in this page because all chains in the apo-structure refer to the same protein.

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48 LYS
106 GLU
107 ARG
110 LEU
141 GLY
142 THR
143 ARG
144 LYS
165 HIS
166 ARG
174 MET
176 LYS
206 GLU
225 MET
227 ASP
254 GLU
256 SER
257 GLY
258 GLY
259 LEU
276 SER
277 THR
278 SER
279 SER
282 GLN
288 ASP
289 PHE
290 SER
291 LEU
292 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:

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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holo-structuresHelp

Table describing the holo-structures and ligands used to define the binding sites.

Column 1 gives the PDB ID of the holo-structure.
Column 2 gives the unique ID of the ligand; a space-separated list of HET-groups that constitute the ligand (see Methods). Each HET-group in the ligand is uniquely identified by a string in which the first four characters are the three-letter HET ID from the PDB file followed by the chain ID from the PISA file, and the last four characters are the residue sequence number from the PDB file.
Column 3 gives the number of atoms in each ligand.
Column 4 gives the number of protein-ligand inter-atomic contacts.

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pdb ID Ligand Unique ID #atoms #contacts
3c2f PRPJ_300 22 80 Details
PRPF_300 22 82
PRPH_300 22 80
PRPD_300 22 80
PRPL_300 22 82
PRPB_300 22 80
3c2v PHTO_301 PRPQ_300 34 133 Details
PHTR_301 PRPN_300 34 133
PHTC_301 PRPE_300 34 142
PHTI_301 PRPK_300 34 142
PHTL_301 PRPH_300 34 142
PHTF_301 PRPB_300 34 142
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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