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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1cwy
TRANSFERASE HEADER
CRYSTAL STRUCTURE OF AMYLOMALTASE FROM THERMUS AQUATICUS, A GLYCOSYLTRANSFERASE CATALYSING THE PRODUCTION OF LARGE CYCLIC GLUCANS TITLE
AMYLOMALTASE 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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52 THR
53 GLY
54 TYR
55 GLY
56 ASP
57 SER
59 TYR
60 GLN
62 PHE
70 TYR
97 TYR
98 GLY
101 TYR
148 LYS
152 GLY
153 GLY
154 LEU
155 PRO
215 PRO
216 ILE
217 PHE
246 VAL
256 GLN
257 ARG
258 TRP
259 GLY
260 ASN
291 ARG
293 ASP
294 HIS
340 GLU
342 LEU
394 HIS
395 ASP
464 ASN
466 PRO
467 GLY
468 ARG
469 PRO
470 SER
471 GLY
472 ASN
473 TRP
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
1esw ACRA_651 EDOA_649 48 145 Details
ACRA_652 44 109
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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