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

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

(click anywhere in this window to remove it)
1ms3
HYDROLASE HEADER
MONOCLINIC FORM OF TRYPANOSOMA CRUZI TRANS-SIALIDASE TITLE
TRANS-SIALIDASE 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).

(click anywhere in this window to remove it)
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.

(click anywhere in this window to remove it)
35 ARG
36 LEU
53 ARG
57 SER
58 PHE
59 ASP
60 ASN
93 ARG
95 VAL
96 ASP
113 TYR
119 TYR
120 TRP
121 THR
176 LEU
179 ALA
195 GLN
203 VAL
229 SER
230 GLU
245 ARG
247 ASP
248 TYR
311 ARG
312 TRP
313 LEU
314 ARG
342 TYR
359 ASN
362 GLU
364 TYR
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:

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)
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.

(click anywhere in this window to remove it)
pdb ID Ligand Unique ID #atoms #contacts
1ms0 DANB_701 LATB_703 43 145 Details
DANA_700 LATA_702 43 151
3b69 BFNA_700 EPEA_701 44 158 Details
1ms8 DANB_701 20 96 Details
DANA_700 20 97
1ms1 DANB2701 GOLB2802 26 120 Details
DANA2700 GOLA2800 GOLA2801 32 138
2ah2 FSIA_700 GOLA1801 GOLA1800 33 141 Details
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: 0.0628 seconds