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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1yvy
LYASE HEADER
CRYSTAL STRUCUTRE OF ANAEROBIOSPIRILLUM SUCCINICIPRODUCENS PHOSPHOENOLPYRUVATE CARBOXYKINASE TITLE
PHOSPHOENOLPYRUVATE CARBOXYKINASE [ATP] 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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60 ARG
200 TYR
205 LYS
206 LYS
225 HIS
243 LEU
244 SER
245 GLY
246 THR
247 GLY
248 LYS
249 THR
250 THR
251 LEU
262 ASP
263 ASP
280 TYR
281 ALA
282 LYS
284 ILE
285 ASN
291 GLU
327 ARG
388 THR
407 PHE
435 THR
443 ARG
444 ILE
446 ILE
449 THR
1060 ARG
1200 TYR
1202 GLY
1205 LYS
1206 LYS
1225 HIS
1243 LEU
1244 SER
1245 GLY
1246 THR
1247 GLY
1248 LYS
1249 THR
1250 THR
1251 LEU
1262 ASP
1263 ASP
1280 TYR
1281 ALA
1282 LYS
1284 ILE
1327 ARG
1388 THR
1407 PHE
1435 THR
1443 ARG
1444 ILE
1445 SER
1446 ILE
1449 THR
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
1ytm ATPB1541 OXDB1543 _MNB1999 _MGB1998 39 155 Details
ATPA_541 _MGA_998 OXDA_543 _MNA_999 39 158
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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