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

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

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3fxy
HYDROLASE HEADER
ACIDIC MAMMALIAN CHINASE, CATALYTIC DOMAIN TITLE
ACIDIC MAMMALIAN CHITINASE COMPND
Illustration of Binding SiteHelp

Figure highlighting the binding site residues. Figures were drawn with Molscript (7) and rendered with Raster3D (8). PISA coordinates (3) are used when available (all entries except NMR).

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Contacting ResiduesHelp

List of binding site residues detected in this protein.

Column 1 gives the position, coloured on a yellow-to-red scale depending on the fraction of corresponding holo-structures where the residue is in contact with a ligand.
Column 2 gives the 3-letter amino acid code, coloured according to physico-chemical type.

Chain ID's of residues are not mentioned in this page because all chains in the apo-structure refer to the same protein.

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27 TYR
29 THR
30 ASN
31 TRP
34 TYR
35 ARG
58 PHE
69 ILE
70 GLU
95 ALA
97 GLY
98 GLY
99 TRP
100 ASN
101 PHE
136 ASP
138 ASP
140 GLU
141 TYR
183 ALA
210 MET
212 TYR
213 ASP
267 TYR
269 HIS
295 ALA
296 LYS
297 GLU
298 SER
300 ILE
302 ALA
358 MET
360 TRP
363 ASP
364 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:

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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holo-structuresHelp

Table describing the holo-structures and ligands used to define the binding sites.

Column 1 gives the PDB ID of the holo-structure.
Column 2 gives the unique ID of the ligand; a space-separated list of HET-groups that constitute the ligand (see Methods). Each HET-group in the ligand is uniquely identified by a string in which the first four characters are the three-letter HET ID from the PDB file followed by the chain ID from the PISA file, and the last four characters are the residue sequence number from the PDB file.
Column 3 gives the number of atoms in each ligand.
Column 4 gives the number of protein-ligand inter-atomic contacts.

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pdb ID Ligand Unique ID #atoms #contacts
3rm8 RM8B_417 23 112 Details
RM8A_417 23 114
3rme GOLA_417 RMEA_418 24 107 Details
GOLB_417 RMEB_418 24 106
3rm4 3RMB___1 22 106 Details
3RMA___1 22 107
3rm9 613A___1 16 85 Details
613B___1 16 96
3fy1 AMIB_803 NAAB_802 NA1B_801 44 148 Details
AMIA_803 NA1A_801 NAAB_802 NA1B_801 NAAA_802 73 244
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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