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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1rex
HYDROLASE (O-GLYCOSYL) HEADER
NATIVE HUMAN LYSOZYME TITLE
LYSOZYME 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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33 LYS
34 TRP
35 GLU
36 SER
37 GLY
39 ASN
42 ALA
43 THR
44 ASN
46 ASN
48 GLY
49 ASP
53 ASP
58 GLN
59 ILE
60 ASN
62 ARG
63 TYR
64 TRP
74 VAL
76 ALA
98 ARG
99 VAL
102 ASP
103 PRO
104 GLN
107 ARG
108 ALA
109 TRP
110 VAL
111 ALA
113 ARG
114 ASN
115 ARG
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
1rez GALA_131 NAGA_132 GOLA_133 30 101 Details
1rem BMAA_131 NAGA_132 PGRA_134 30 100 Details
1lzs NAGB_136 NAGB_138 NAGB_137 43 92 Details
NAGA_136 NAGA_139 NAGA_138 NAGA_137 NAGA_140 NAGA_141 86 217
1rey GOLA_133 NAGA_132 NAGA_131 33 110 Details
1re2 GALA_131 NAGA_134 NAGA_132 GALA_133 GOLA_136 GOLA_135 60 157 Details
1lzr NAGA_136 NAGA_138 NAGA_137 43 90 Details
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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