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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3b4p
BIOSYNTHETIC PROTEIN HEADER
CRYSTAL STRUCTURE OF PHENAZINE BIOSYNTHESIS PROTEIN PHZA/B FROM BURKHOLDERIA CEPACIA R18194, COMPLEX WITH 2- (CYCLOHEXYLAMINO)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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AZI C 600
30A TYR
33A THR
38A ARG
41A ARG
77A SER
84A TRP
86A TRP
140A GLU
ACT F 600
30D TYR
33D THR
38D ARG
41D ARG
77D SER
84D TRP
86D TRP
3B4 B 500
38A 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
160D ARG
163D LEU
3B4 E 500
52D GLY
53D LEU
62D ILE
64D ILE
73D HIS
76D TRP
77D SER
81D PHE
84D TRP
86D TRP
112D PHE
120D TYR
124D PHE
140D GLU
142D MET
147D GLN
160A ARG
163A 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
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
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
3jup AKDB_500 Details
AKDA_500
3jun AJDB_500 AKDB_600 Details
AJDA_500 AKDA_600
3jum AODB_500 Details
AODA_500
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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3B4 NAME: not_found
FORMULA: not_found
SMILES: not_found
AZI NAME: AZIDE ION
FORMULA: N3
SMILES: [N-]=[N+]=[N-]
ACT NAME: ACETATE ION
FORMULA: C2 H3 O2
SMILES: CC([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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