university lille north of france LigASite database of binding sites
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LigASite v9.7 (nr25) - non-redundant
LigASite v9.7 (redundant) - redundant
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Browse dataset
holo-structureHelp

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

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1of8
LYASE HEADER
DOUBLE COMPLEX OF THE TYROSINE SENSITIVE DAHP SYNTHASE FROM S. CEREVISIAE WITH CO2+, PEP AND THE E4P ANALOGOUE G3P 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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G3P D1371
76A CYS
112A LYS
113A PRO
114A ARG
115A THR
116A THR
117A VAL
180A ARG
282A HIS
341A THR
342A ASP
CO B1369
76A CYS
112A LYS
282A HIS
316A GLU
342A ASP
G3P I1374
76F CYS
112F LYS
113F PRO
114F ARG
115F THR
116F THR
117F VAL
180F ARG
282F HIS
341F THR
342F ASP
CO G1372
76F CYS
112F LYS
282F HIS
316F GLU
342F ASP
G3P N1371
76K CYS
112K LYS
113K PRO
114K ARG
115K THR
116K THR
117K VAL
180K ARG
282K HIS
341K THR
342K ASP
CO L1369
76K CYS
112K LYS
282K HIS
316K GLU
342K ASP
G3P S1374
76P CYS
112P LYS
113P PRO
114P ARG
115P THR
116P THR
117P VAL
180P ARG
282P HIS
341P THR
342P ASP
CO Q1372
76P CYS
112P LYS
282P HIS
316P GLU
342P ASP
PEP C1370
107A ARG
109A TYR
112A LYS
113A PRO
158A GLU
178A GLY
179A ALA
180A ARG
201A LYS
249A ARG
282A HIS
314A MET
PEP H1373
107F ARG
109F TYR
112F LYS
113F PRO
158F GLU
178F GLY
179F ALA
180F ARG
201F LYS
249F ARG
282F HIS
314F MET
PEP M1370
107K ARG
109K TYR
112K LYS
113K PRO
158K GLU
178K GLY
179K ALA
180K ARG
201K LYS
249K ARG
282K HIS
PEP R1373
107P ARG
109P TYR
112P LYS
113P PRO
158P GLU
178P GLY
179P ALA
180P ARG
201P LYS
249P ARG
282P HIS
314P MET
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:

» PDB
» CSA
» PDBSum
» CATH
» Scop
» Pfam
» UniProt

LigPlot (hosted at the EBI):

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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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» XML File
» XML Schema
» Coordinates (PDB)
» apo binding site (PDB)
» holo binding site (PDB)
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
1ofa GOLQ_603 PEPP_508 _COO_400 Details
GOLH_603 PEPG_508 _COF_400
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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G3P NAME: 3-PHOSPHOGLYCEROL
FORMULA: C3 H9 O6 P1
SMILES: OCC(O)COP(O)(O)=O
CO NAME: COBALT (II) ION
FORMULA: CO1
SMILES: [Co++]
PEP NAME: PHOSPHOENOLPYRUVATE
FORMULA: C3 H5 O6 P1
SMILES: OC(=O)C(=C)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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