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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3b9a
HYDROLASE HEADER
CRYSTAL STRUCTURE OF VIBRIO HARVEYI CHITINASE A COMPLEXED WITH HEXASACCHARIDE TITLE
CHITINASE A 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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NAG A 702
164A TYR
192A PHE
274A GLY
275A TRP
313A ASP
315A MET
363A ALA
389A MET
391A TYR
392A ASP
461A TYR
463A ARG
570A TRP
NAG A 703
168A TRP
173A ARG
192A PHE
205A VAL
273A GLY
274A GLY
275A TRP
276A THR
461A TYR
463A ARG
498A GLU
501A VAL
570A TRP
571A GLU
NAG A 704
168A TRP
173A ARG
192A PHE
205A VAL
209A SER
228A HIS
276A THR
277A LEU
497A TRP
498A GLU
NAG A 700
275A TRP
316A PHE
320A GLY
365A GLY
366A VAL
367A GLY
370A LYS
389A MET
391A TYR
392A ASP
393A PHE
397A TRP
435A TYR
NAG A 701
275A TRP
315A MET
316A PHE
365A GLY
389A MET
391A TYR
392A ASP
397A TRP
463A ARG
498A GLU
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
3b9e Details
other holo-structures
pdb ID Ligand Unique ID
3b9d NAGA_700 NAGA_701 NAGA_703 NAGA_702 Details
NAGA_703 NAGA_702
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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NAG NAME: N-ACETYL-D-GLUCOSAMINE
FORMULA: C8 H15 N1 O6
SMILES: CC(=O)NC1C(O)OC(CO)C(O)C1O
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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