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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1ofa
LYASE HEADER
CRYSTAL STRUCTURE OF THE TYROSINE-REGULATED 3-DEOXY-D-ARABINO-HEPTULOSONATE-7-PHOSPHATE SYNTHASE FROM SACCHAROMYCES CEREVISIAE IN COMPLEX WITH PHOSPHOENOLPYRUVATE AND COBALT(II) TITLE
PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE 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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GOL Q 603
76N CYS
112N LYS
113N PRO
114N ARG
115N THR
180N ARG
282N HIS
341N THR
342N ASP
CO O 400
76N CYS
282N HIS
316N GLU
342N ASP
GOL H 603
76E CYS
112E LYS
113E PRO
114E ARG
115E THR
180E ARG
282E HIS
341E THR
342E ASP
CO F 400
76E CYS
282E HIS
316E GLU
342E ASP
PEP P 508
107N ARG
109N TYR
112N LYS
113N PRO
158N GLU
178N GLY
179N ALA
180N ARG
201N LYS
249N ARG
282N HIS
PEP G 508
107E ARG
109E TYR
112E LYS
113E PRO
158E GLU
178E GLY
179E ALA
180E ARG
201E LYS
249E ARG
282E HIS
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).

Clicking the blue 'Hide table of related structures' button removes the entire table.

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apo-structure
pdb ID
1ofp Details
other holo-structures
pdb ID Ligand Unique ID
1of8 G3PD1371 _COB1369 PEPC1370 Details
G3PI1374 PEPH1373 _COG1372
G3PN1371 _COL1369 PEPM1370
G3PS1374 PEPR1373 _COQ1372
1ofr PHEE1002 Details
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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GOL NAME: GLYCEROL
FORMULA: C3 H8 O3
SMILES: OCC(O)CO
PEP NAME: PHOSPHOENOLPYRUVATE
FORMULA: C3 H5 O6 P1
SMILES: OC(=O)C(=C)OP(O)(O)=O
CO NAME: COBALT (II) ION
FORMULA: CO1
SMILES: [Co++]
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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