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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1i1h
ISOMERASE HEADER
CRYSTAL STRUCTURE ANALYSIS OF PRECORRIN-8X METHYLMUTASE COMPLEX WITH HYDROGENOBYRINIC ACID TITLE
PRECORRIN-8X METHYLMUTASE 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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COJ B1121
10C GLY
11C ASN
13C ILE
14C TYR
17C SER
40C ARG
43C HIS
44C ALA
78A ALA
80A MET
84C GLY
85C VAL
86C THR
87C ARG
88C ALA
89C ARG
100A LEU
101A ARG
115A THR
116A ARG
117A SER
137A ASN
138A ALA
139A PRO
140A THR
164A VAL
165A GLY
166A PHE
167A VAL
169A ALA
195C SER
196C ALA
199C ALA
200C ALA
203C ASN
COJ D1121
10A GLY
11A ASN
13A ILE
14A TYR
17A SER
40A ARG
43A HIS
44A ALA
78C ALA
80C MET
84A GLY
85A VAL
86A THR
87A ARG
88A ALA
89A ARG
100C LEU
101C ARG
115C THR
116C ARG
117C SER
137C ASN
138C ALA
139C PRO
140C THR
164C VAL
165C GLY
166C PHE
167C VAL
169C ALA
195A SER
196A ALA
199A ALA
200A ALA
203A ASN
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
1f2v 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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COJ NAME: HYDROGENOBYRINIC ACID
FORMULA: C45 H60 N4 O14
SMILES: CC1=C2NC(C)(C3N=C(C(=C4N=C(C=C5N=C1C(C)(CC(O)=O)C5CCC(O)=O)C(C)(C)C4CCC(O)=O)C)C(C)(CCC(O)=O)C3CC(O)=O)C(C)(CC(O)=O)C2CCC(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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