university lille north of france LigASite database of binding sites
holo-structureHelp

PDB ID and HEADER, TITLE and COMPND records of the PDB file.

(click anywhere in this window to remove it)
1u80
LIGASE HEADER
PHOSPHOPANTOTHENOYLCYSTEINE SYNTHETASE FROM E. COLI, CMP COMPLEX TITLE
COENZYME A BIOSYNTHESIS BIFUNCTIONAL PROTEIN 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.

(click anywhere in this window to remove it)
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.

(click anywhere in this window to remove it)
C5P C2500
194A THR
271A PHE
273A GLY
274A CYS
275A ALA
276A ALA
277A VAL
278A ALA
279A ASP
289D LYS
307A ASN
308A PRO
309A ASP
310A ILE
311A VAL
326A GLY
327A PHE
328A ALA
329A ALA
330A GLU
341A LYS
345A LYS
347A LEU
C5P F2500
194D THR
271D PHE
273D GLY
274D CYS
275D ALA
276D ALA
277D VAL
278D ALA
279D ASP
289A LYS
307D ASN
308D PRO
309D ASP
310D ILE
311D VAL
326D GLY
327D PHE
328D ALA
329D ALA
330D GLU
341D LYS
345D LYS
347D 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.

(click anywhere in this window to remove it)

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.

(click anywhere in this window to remove it)
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.

(click anywhere in this window to remove it)
apo-structure
pdb ID
1u7u Details
other holo-structures
pdb ID Ligand Unique ID
1u7z PMTB_500 Details
PMTD1500
1u7w CTPF1500 _CAE1501 Details
CTPC_500 _CAB_501
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.

(click anywhere in this window to remove it)
C5P NAME: CYTIDINE-5'-MONOPHOSPHATE
FORMULA: C9 H14 N3 O8 P1
SMILES: NC1=NC(=O)N(C=C1)C2OC(COP(O)(O)=O)C(O)C2O
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
Script execution time: 0.0763 seconds