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

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

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3i0c
TRANSFERASE HEADER
CRYSTAL STRUCTURE OF GTB C80S/C196S UNLIGANDED TITLE
ABO GLYCOSYLTRANSFERASE COMPND
Illustration of Binding SiteHelp

Figure highlighting the binding site residues. Figures were drawn with Molscript (7) and rendered with Raster3D (8). PISA coordinates (3) are used when available (all entries except NMR).

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Contacting ResiduesHelp

List of binding site residues detected in this protein.

Column 1 gives the position, coloured on a yellow-to-red scale depending on the fraction of corresponding holo-structures where the residue is in contact with a ligand.
Column 2 gives the 3-letter amino acid code, coloured according to physico-chemical type.

Chain ID's of residues are not mentioned in this page because all chains in the apo-structure refer to the same protein.

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72 PRO
74 PRO
75 LYS
78 THR
79 PRO
80 SER
85 LEU
87 VAL
89 PRO
97 GLU
98 GLY
99 THR
100 PHE
101 ASN
102 ILE
121 PHE
122 ALA
123 ILE
124 LYS
125 LYS
126 TYR
188 ARG
210 VAL
211 ASP
212 VAL
213 ASP
214 MET
233 HIS
234 PRO
235 SER
236 PHE
245 THR
264 TYR
266 MET
267 GLY
268 ALA
300 TRP
301 HIS
302 ASP
303 GLU
325 TRP
326 ASP
329 LEU
330 LEU
343 ALA
346 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:

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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holo-structuresHelp

Table describing the holo-structures and ligands used to define the binding sites.

Column 1 gives the PDB ID of the holo-structure.
Column 2 gives the unique ID of the ligand; a space-separated list of HET-groups that constitute the ligand (see Methods). Each HET-group in the ligand is uniquely identified by a string in which the first four characters are the three-letter HET ID from the PDB file followed by the chain ID from the PISA file, and the last four characters are the residue sequence number from the PDB file.
Column 3 gives the number of atoms in each ligand.
Column 4 gives the number of protein-ligand inter-atomic contacts.

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pdb ID Ligand Unique ID #atoms #contacts
3i0d UDPD___1 25 73 Details
UDPB___1 25 74
3i0g UDPC_357 25 74 Details
UDPJ_357 25 72
_MNK___2 UDPI_358 25 80
BHGL___1 FUCN_356 _MNK___2 GALM_359 UDPI_358 64 167
BHGE___1 _MND___2 GALF_359 UDPB_358 FUCG_356 64 165
3i0f __UA___1 17 70 Details
BHGI_400 UDPG_357 _MNH___2 FUCJ_356 54 154
BHGD_400 UDPB_357 FUCE_356 _MNC___2 54 149
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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