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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1ffq
HYDROLASE HEADER
CRYSTAL STRUCTURE OF CHITINASE A COMPLEXED WITH ALLOSAMIDIN 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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AMI H 3
163E TYR
191E PHE
275E TRP
313E ASP
315E GLU
362E ALA
388E MET
390E TYR
391E ASP
444E TYR
446E ARG
537E PHE
539E TRP
AMI D 3
163A TYR
191A PHE
275A TRP
313A ASP
315A GLU
362A ALA
388A MET
390A TYR
391A ASP
444A TYR
446A ARG
537A PHE
539A TRP
NAA F 1
167E TRP
172E ARG
191E PHE
204E LEU
207E ILE
210E SER
229E HIS
276E THR
277E LEU
472E TRP
473E GLU
NAA G 2
167E TRP
172E ARG
191E PHE
207E ILE
274E GLY
275E TRP
276E THR
444E TYR
446E ARG
473E GLU
476E ILE
539E TRP
540E GLU
NAA B 1
167A TRP
172A ARG
191A PHE
204A LEU
207A ILE
210A SER
229A HIS
276A THR
277A LEU
472A TRP
473A GLU
NAA C 2
167A TRP
172A ARG
191A PHE
207A ILE
274A GLY
275A TRP
276A THR
444A TYR
446A ARG
473A GLU
476A ILE
539A TRP
540A 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
1edq 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.

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AMI NAME: ALLOSAMIZOLINE
FORMULA: C9 H16 N2 O4
SMILES: CN(C)C1=NC2C(O)C(O)C(CO)C2O1
NAA NAME: N-ACETYL-D-ALLOSAMINE
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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