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

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

(click anywhere in this window to remove it)
1esw
TRANSFERASE HEADER
X-RAY STRUCTURE OF ACARBOSE BOUND TO AMYLOMALTASE FROM THERMUS AQUATICUS. IMPLICATIONS FOR THE SYNTHESIS OF LARGE CYCLIC GLUCANS TITLE
AMYLOMALTASE 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.

(click anywhere in this window to remove it)
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.

(click anywhere in this window to remove it)
ACR A 652
52A THR
53A GLY
54A TYR
55A GLY
56A ASP
62A PHE
70A TYR
97A TYR
98A GLY
101A TYR
148A LYS
152A GLY
153A GLY
154A LEU
155A PRO
469A PRO
470A SER
471A GLY
ACR A 651
57A SER
59A TYR
60A GLN
246A VAL
256A GLN
257A ARG
258A TRP
259A GLY
260A ASN
291A ARG
293A ASP
294A HIS
340A GLU
342A LEU
394A HIS
395A ASP
464A ASN
466A PRO
467A GLY
468A ARG
472A ASN
473A TRP
EDO A 649
59A TYR
215A PRO
216A ILE
217A PHE
258A TRP
260A ASN
293A ASP
294A HIS
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:

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.

(click anywhere in this window to remove it)
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.

(click anywhere in this window to remove it)
apo-structure
pdb ID
1cwy 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.

(click anywhere in this window to remove it)
ACR NAME: ACARBOSE
FORMULA: C25 H43 N1 O18
SMILES: CC1OC(OC2C(O)C(O)C(OC2CO)OC3C(O)C(O)C(O)OC3CO)C(O)C(O)C1NC4C=C(CO)C(O)C(O)C4O
EDO NAME: 1,2-ETHANEDIOL
FORMULA: C2 H6 O2
SMILES: OCCO
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: 0.0381 seconds