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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1ll4
HYDROLASE HEADER
STRUCTURE OF C. IMMITIS CHITINASE 1 COMPLEXED WITH ALLOSAMIDIN TITLE
CHITINASE 1 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 C 503
43C TYR
71C PHE
131C TRP
169C ASP
171C GLU
211C ALA
237C MET
239C TYR
240C ASP
293C TYR
295C ARG
376C MET
378C TRP
AMI A 503
43A TYR
71A PHE
131A TRP
169A ASP
171A GLU
211A ALA
237A MET
239A TYR
240A ASP
293A TYR
295A ARG
376A MET
378A TRP
AMI D 503
43D TYR
71D PHE
131D TRP
169D ASP
171D GLU
211D ALA
237D MET
239D TYR
240D ASP
293D TYR
295D ARG
376D MET
378D TRP
AMI B 503
43B TYR
71B PHE
131B TRP
169B ASP
171B GLU
211B ALA
237B MET
239B TYR
240B ASP
293B TYR
295B ARG
376B MET
378B TRP
NAA C 502
47C TRP
52C ARG
71C PHE
130C GLY
131C TRP
132C THR
133C TYR
293C TYR
295C ARG
316C GLU
319C VAL
378C TRP
379C GLU
NAA C 501
47C TRP
52C ARG
71C PHE
132C THR
133C TYR
315C TRP
316C GLU
NAA A 502
47A TRP
52A ARG
71A PHE
130A GLY
131A TRP
132A THR
293A TYR
295A ARG
316A GLU
319A VAL
378A TRP
379A GLU
NAA A 501
47A TRP
52A ARG
71A PHE
132A THR
133A TYR
315A TRP
316A GLU
NAA D 502
47D TRP
52D ARG
71D PHE
130D GLY
131D TRP
132D THR
293D TYR
295D ARG
316D GLU
319D VAL
378D TRP
379D GLU
NAA D 501
47D TRP
52D ARG
71D PHE
132D THR
133D TYR
315D TRP
316D GLU
NAA B 501
47B TRP
52B ARG
71B PHE
132B THR
133B TYR
315B TRP
316B GLU
NAA B 502
47B TRP
52B ARG
71B PHE
130B GLY
131B TRP
132B THR
293B TYR
295B ARG
316B GLU
319B VAL
378B TRP
379B 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
1d2k 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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