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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1ytm
LYASE HEADER
CRYSTAL STRUCTURE OF PHOSPHOENOLPYRUVATE CARBOXYKINASE OF ANAEROBIOSPIRILLUM SUCCINICIPRODUCENS COMPLEXED WITH ATP, OXALATE, MAGNESIUM AND MANGANESE IONS TITLE
PHOSPHOENOLPYRUVATE CARBOXYKINASE [ATP] 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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OXD A 543
60A ARG
200A TYR
205A LYS
206A LYS
225A HIS
244A SER
263A ASP
280A TYR
327A ARG
388A THR
407A PHE
MN A 999
206A LYS
225A HIS
263A ASP
ATP A 541
225A HIS
243A LEU
244A SER
245A GLY
246A THR
247A GLY
248A LYS
249A THR
250A THR
251A LEU
263A ASP
280A TYR
282A LYS
284A ILE
285A ASN
291A GLU
327A ARG
435A THR
443A ARG
444A ILE
446A ILE
449A THR
MG A 998
249A THR
262A ASP
263A ASP
280A TYR
281A ALA
327A ARG
OXD B1543
1060B ARG
1200B TYR
1202B GLY
1205B LYS
1206B LYS
1225B HIS
1244B SER
1263B ASP
1280B TYR
1327B ARG
1388B THR
1407B PHE
MN B1999
1206B LYS
1225B HIS
1263B ASP
ATP B1541
1225B HIS
1243B LEU
1244B SER
1245B GLY
1246B THR
1247B GLY
1248B LYS
1249B THR
1250B THR
1251B LEU
1263B ASP
1280B TYR
1282B LYS
1284B ILE
1327B ARG
1435B THR
1443B ARG
1444B ILE
1445B SER
1446B ILE
1449B THR
MG B1998
1249B THR
1262B ASP
1263B ASP
1280B TYR
1281B ALA
1327B ARG
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).

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apo-structure
pdb ID
1yvy Details
other holo-structures
pdb ID Ligand Unique ID
none
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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ATP NAME: ADENOSINE-5'-TRIPHOSPHATE
FORMULA: C10 H16 N5 O13 P3
SMILES: Nc1ncnc2[n](cnc12)C3OC(COP(O)(=O)OP(O)(=O)OP(O)(O)=O)C(O)C3O
OXD NAME: OXALIC ACID
FORMULA: C2 H2 O4
SMILES: OC(=O)C(O)=O
MN NAME: MANGANESE (II) ION
FORMULA: MN1
SMILES: [Mn++]
MG NAME: MAGNESIUM ION
FORMULA: MG1
SMILES: [Mg++]
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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