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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3jum
BIOSYNTHETIC PROTEIN HEADER
CRYSTAL STRUCTURE OF PHZA/B FROM BURKHOLDERIA CEPACIA R18194 IN COMPLEX WITH 5-BROMO-2-((1S,3R)-3- CARBOXYCYCLOHEXYLAMINO)BENZOIC ACID TITLE
PHENAZINE BIOSYNTHESIS PROTEIN A/B 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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AOD B 500
30B TYR
38B ARG
41B ARG
52B GLY
53B LEU
62B ILE
64B ILE
73B HIS
76B TRP
77B SER
81B PHE
84B TRP
86B TRP
112B PHE
120B TYR
124B PHE
140B GLU
142B MET
147B GLN
160A ARG
163A LEU
AOD A 500
30A TYR
38A ARG
41A ARG
52A GLY
53A LEU
62A ILE
64A ILE
73A HIS
76A TRP
77A SER
81A PHE
84A TRP
86A TRP
112A PHE
120A TYR
124A PHE
140A GLU
142A MET
147A GLN
160B ARG
163B LEU
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
3ex9 Details
other holo-structures
pdb ID Ligand Unique ID
3cnm ACTF_600 HHAG_500 Details
ACTB_600 HHAD_500
3juo AJDB_500 Details
AJDA_500
3dzl 3OCB_500 3OCB_600 Details
3OCA_500 3OCA_600
3b4p 3B4B_500 AZIC_600 Details
3B4E_500 ACTF_600
3jup AKDB_500 Details
AKDA_500
3jun AJDB_500 AKDB_600 Details
AJDA_500 AKDA_600
3juq AJDA_500 AKDA_600 Details
AKDB_600
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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AOD NAME: not_found
FORMULA: not_found
SMILES: not_found
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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