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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2zcr
TRANSFERASE HEADER
CRYSTAL STRUCTURE OF THE C(30) CAROTENOID DEHYDROSQUALENE SYNTHASE FROM STAPHYLOCOCCUS AUREUS COMPLEXED WITH BISPHOSPHONATE BPH-698 TITLE
DEHYDROSQUALENE SYNTHASE 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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B69 A 668
18A HIS
22A PHE
26A PHE
41A TYR
45A ARG
48A ASP
129A TYR
133A VAL
134A ALA
137A VAL
138A GLY
141A LEU
142A THR
145A LEU
157A ALA
160A LEU
161A GLY
164A LEU
165A GLN
168A ASN
169A ILE
171A ARG
172A ASP
175A GLU
176A ASP
183A TYR
233A PHE
241A ILE
244A ALA
248A TYR
265A ARG
MG A 669
168A ASN
172A ASP
175A GLU
176A ASP
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
Help

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
2zco Details
other holo-structures
pdb ID Ligand Unique ID
3nri DH7A_288 Details
3acx 673A1001 Details
3acy 702A1001 _MGA1002 Details
2zy1 830A_808 Details
2zcq B65A_451 _MGA_453 _MGA_452 Details
2zcs B70A_640 Details
3npr PS7A1001 _MGA1002 Details
3acw 651A1001 Details
2zcp FPSA_657 FPSA_658 _MGA_661 _MGA_663 _MGA_662 Details
FPSB_659 _MGB_665 _MGB_666 FPSB_660 _MGB_664
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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B69 NAME: not_found
FORMULA: not_found
SMILES: not_found
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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