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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1h7t
TRANSFERASE HEADER
THE STRUCTURE OF CMP:2-KETO-3-DEOXY-MANNO-OCTONIC ACID SYNTHETASE AND OF ITS COMPLEXES WITH SUBSTRATES AND SUBSTRATE ANALOGUES, HERE COMPLEX WITH CMP-NEUAC, CMP-NEUAC COMPLEX TITLE
3-DEOXY-MANNO-OCTULOSONATE CYTIDYLYLTRANSFERASE 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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C5P C1242
8B PRO
9B ALA
10B ARG
13B SER
19B LYS
73B HIS
74B GLU
75B SER
76B GLY
79B ARG
96B GLN
97B GLY
98B ASP
SIA D1243
13B SER
19B LYS
96B GLN
98B ASP
99B GLU
171B LYS
174B GLY
175B ILE
221B GLY
222B PRO
223B GLY
224B VAL
225B ASP
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
1h7e Details
other holo-structures
pdb ID Ligand Unique ID
1h7h CDPB1246 Details
CDPD1242
1h7f C5PC1242 Details
1h7g CTPD1243 _MGC1242 Details
1gq9 CTPF1243 _MGE1242 Details
CTPC1243 _MGB1242
1gqc C5PF1243 _MGE1242 Details
CMKC1244 _MGB1243
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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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
SIA NAME: O-SIALIC ACID
FORMULA: C11 H19 N1 O9
SMILES: CC(=O)NC1C(O)CC(O)(OC1C(O)C(O)CO)C(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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