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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1p5r
TRANSFERASE HEADER
FORMYL-COA TRANSFERASE IN COMPLEX WITH COENZYME A TITLE
FORMYL-COENZYME A 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
15A HIS
16A VAL
17A GLN
18A ALA
36A ILE
37A GLU
38A ARG
44A MET
72A LEU
73A ASP
74A MET
75A LYS
96A ASN
97A PHE
98A GLY
99A PRO
101A ALA
104A ARG
105A MET
124A VAL
125A LYS
126A GLY
136A LEU
137A LYS
138A VAL
139A TYR
169A ASP
200A MET
287C ASN
288C MET
COA D 502
15C HIS
16C VAL
17C GLN
18C ALA
36C ILE
37C GLU
38C ARG
44C MET
72C LEU
73C ASP
74C MET
75C LYS
96C ASN
97C PHE
98C GLY
99C PRO
101C ALA
104C ARG
105C MET
124C VAL
125C LYS
126C GLY
136C LEU
137C LYS
138C VAL
139C TYR
140C GLU
169C ASP
200C MET
287A ASN
346A PRO
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
1p5h 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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