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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1xvt
TRANSFERASE HEADER
CRYSTAL STRUCTURE OF NATIVE CAIB IN COMPLEX WITH COENZYME A TITLE
CROTONOBETAINYL-COA:CARNITINE COA-TRANSFERASE 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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COA B 501
20A SER
22A ILE
23A GLU
24A ILE
25A ALA
26A GLY
43A ILE
44A GLU
45A ASN
71A LEU
72A ASN
73A ILE
74A PHE
95A ALA
96A SER
97A LYS
100A ALA
101A PHE
103A ARG
104A ARG
123A LEU
124A SER
125A GLY
137A LEU
138A PRO
139A ALA
140A TYR
169A ASP
255C GLN
316C ASN
COA D 501
20C SER
22C ILE
23C GLU
24C ILE
25C ALA
26C GLY
43C ILE
44C GLU
45C ASN
71C LEU
72C ASN
73C ILE
74C PHE
95C ALA
96C SER
97C LYS
100C ALA
101C PHE
103C ARG
104C ARG
123C LEU
124C SER
125C GLY
137C LEU
138C PRO
139C ALA
140C TYR
169C ASP
255A GLN
316A 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
1xk6 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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COA NAME: COENZYME A
FORMULA: C21 H36 N7 O16 P3 S1
SMILES: CC(C)(COP(O)(=O)OP(O)(=O)OCC1OC(C(O)C1OP(O)(O)=O)[n]2cnc3c(N)ncnc23)C(O)C(=O)NCCC(=O)NCCS
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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