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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3f47
OXIDOREDUCTASE HEADER
THE CRYSTAL STRUCTURE OF [FE]-HYDROGENASE (HMD) HOLOENZYME FROM METHANOCALDOCOCCUS JANNASCHII TITLE
5,10-METHENYLTETRAHYDROMETHANOPTERIN HYDROGENASE; 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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I2C F 359
6F LEU
7F GLY
9F GLY
10F CYS
13F THR
14F HIS
42F SER
63F SER
64F ASP
65F PRO
114F PRO
115F PRO
118F CYS
135F ASP
148F TRP
149F LEU
150F PRO
151F LYS
158F ILE
175F ALA
176F CYS
177F THR
202F PRO
205F VAL
I2C A 359
6A LEU
7A GLY
9A GLY
10A CYS
13A THR
14A HIS
42A SER
63A SER
64A ASP
65A PRO
114A PRO
115A PRO
118A CYS
135A ASP
148A TRP
149A LEU
150A PRO
151A LYS
158A ILE
175A ALA
176A CYS
177A THR
202A PRO
205A VAL
CMO J 361
14F HIS
148F TRP
204F CYS
205F VAL
206F PRO
CMO E 361
14A HIS
148A TRP
204A CYS
205A VAL
206A PRO
CMO I 362
176F CYS
201F HIS
202F PRO
203F GLY
204F CYS
FE2 H 360
176F CYS
CMO D 362
176A CYS
201A HIS
202A PRO
203A GLY
204A CYS
FE2 C 360
176A CYS
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).

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apo-structure
pdb ID
2b0j Details
other holo-structures
pdb ID Ligand Unique ID
none
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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CMO NAME: CARBON MONOXIDE
FORMULA: C1 O1
SMILES: C=O
FE2 NAME: FE (II) ION
FORMULA: FE1
SMILES: [Fe++]
I2C 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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