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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2qx7
PLANT PROTEIN HEADER
STRUCTURE OF EUGENOL SYNTHASE FROM OCIMUM BASILICUM TITLE
EUGENOL SYNTHASE 1 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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NAP B 401
14B GLY
16B THR
17B GLY
18B TYR
19B ILE
37B PHE
38B THR
39B ARG
44B LYS
62B GLU
63B LEU
82B ALA
83B LEU
84B ALA
85B PHE
87B GLN
88B ILE
90B ASP
110B SER
111B ASP
112B PHE
113B GLY
132B LYS
152B ASN
153B CYS
154B PHE
157B TYR
158B PHE
265B LEU
312B ALA
313B ALA
NAP A 401
14A GLY
16A THR
17A GLY
18A TYR
19A ILE
37A PHE
38A THR
39A ARG
44A LYS
62A GLU
63A LEU
82A ALA
83A LEU
84A ALA
85A PHE
87A GLN
88A ILE
90A ASP
110A SER
111A ASP
112A PHE
113A GLY
132A LYS
152A ASN
153A CYS
154A PHE
157A TYR
158A PHE
265A LEU
312A ALA
313A ALA
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
2qys Details
other holo-structures
pdb ID Ligand Unique ID
2r6j NDPB_401 Details
NDPA_401
2qzz EMFA_601 NAPA_401 Details
EMFB_602 NAPB_401
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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NAP NAME: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
FORMULA: C21 H28 N7 O17 P3
SMILES: NC(=O)c1ccc[n+](c1)C2OC(COP([O-])(=O)OP(O)(=O)OCC3OC(C(OP(O)(O)=O)C3O)[n]4cnc5c(N)ncnc45)C(O)C2O
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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