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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2ggq
TRANSFERASE HEADER
COMPLEX OF HYPOTHETICAL GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE FROM SULFOLOBUS TOKODAII TITLE
401AA LONG HYPOTHETICAL GLUCOSE-1-PHOSPHATE 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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TTP B 500
6A LEU
7A ALA
8A ALA
9A GLY
10A SER
11A GLY
12A GLU
13A ARG
14A LEU
23A LYS
73A GLN
78A LYS
79A GLY
80A THR
83A ALA
97A TYR
99A ASP
147A LYS
179A ARG
181A GLU
210A GLY
344A LYS
TTP L 500
6K LEU
7K ALA
8K ALA
9K GLY
10K SER
11K GLY
12K GLU
13K ARG
14K LEU
23K LYS
73K GLN
78K LYS
79K GLY
80K THR
83K ALA
97K TYR
99K ASP
147K LYS
179K ARG
181K GLU
210K GLY
344K LYS
TTP G 500
6F LEU
8F ALA
9F GLY
10F SER
11F GLY
12F GLU
13F ARG
14F LEU
23F LYS
73F GLN
78F LYS
79F GLY
80F THR
83F ALA
97F TYR
99F ASP
147F LYS
179F ARG
181F GLU
210F GLY
344F LYS
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
2ggo 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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TTP NAME: THYMIDINE-5'-TRIPHOSPHATE
FORMULA: C10 H17 N2 O14 P3
SMILES: CC1=CN(C2CC(O)C(COP(O)(=O)OP(O)(=O)OP(O)(O)=O)O2)C(=O)NC1=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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