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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3fy1
HYDROLASE HEADER
THE ACIDIC MAMMALIAN CHITINASE CATALYTIC DOMAIN IN COMPLEX WITH METHYLALLOSAMIDIN TITLE
ACIDIC MAMMALIAN CHITINASE 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 B 803
27B TYR
58B PHE
95B ALA
98B GLY
99B TRP
136B ASP
138B ASP
140B GLU
183B ALA
210B MET
212B TYR
213B ASP
267B TYR
358B MET
360B TRP
AMI A 803
27A TYR
58A PHE
98A GLY
99A TRP
136A ASP
138A ASP
140A GLU
183A ALA
210A MET
212A TYR
213A ASP
267A TYR
358A MET
360A TRP
NA1 A 801
30A ASN
31A TRP
34A TYR
58A PHE
69A ILE
70B GLU
100A ASN
295A ALA
296A LYS
297A GLU
298A SER
NAA B 802
31B TRP
35B ARG
58B PHE
97B GLY
98B GLY
99B TRP
100B ASN
101B PHE
213B ASP
267B TYR
297B GLU
300B ILE
360B TRP
364B LEU
NA1 B 801
31B TRP
34B TYR
58B PHE
69B ILE
70A GLU
100B ASN
295B ALA
296B LYS
297B GLU
298B SER
NAA A 802
31A TRP
35A ARG
58A PHE
97A GLY
98A GLY
99A TRP
100A ASN
101A PHE
213A ASP
267A TYR
297A GLU
300A ILE
360A TRP
364A LEU
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
3fxy Details
other holo-structures
pdb ID Ligand Unique ID
3rm8 RM8B_417 Details
RM8A_417
3rme GOLA_417 RMEA_418 Details
GOLB_417 RMEB_418
3rm4 3RMB___1 Details
3RMA___1
3rm9 613A___1 Details
613B___1
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
NA1 NAME: METHYL N-ACETYL ALLOSAMINE
FORMULA: C9 H17 N1 O6
SMILES: COCC1OC(O)C(NC(C)=O)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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