university lille north of france LigASite database of binding sites
Home
News
Introduction
Methods
Flow Chart
References
Download
About
FAQ
Search
LigASite v4.0 (nr25) - non-redundant
LigASite v4.0 (redundant) - redundant
(click to remove window)
Browse dataset
apo-structureHelp

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

(click anywhere in this window to remove it)
1vds
HYDROLASE HEADER
THE CRYSTAL STRUCTURE OF THE TETRAGONAL FORM OF HEN EGG WHITE LYSOZYME AT 1.6 ANGSTROMS RESOLUTION IN SPACE TITLE
LYSOZYME C 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).

(click anywhere in this window to remove it)
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.

(click anywhere in this window to remove it)
5 ARG
34 PHE
35 GLU
44 ASN
45 ARG
46 ASN
47 THR
48 ASP
50 SER
52 ASP
56 LEU
57 GLN
58 ILE
59 ASN
61 ARG
62 TRP
63 TRP
73 ARG
75 LEU
98 ILE
101 ASP
102 GLY
103 ASN
104 GLY
106 ASN
107 ALA
108 TRP
109 VAL
110 ALA
112 ARG
114 ARG
117 GLY
118 THR
119 ASP
122 ALA
123 TRP
125 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.

(click anywhere in this window to remove it)

Links to external databases:

» PDB
» CSA
» PDBSum
» CATH
» Scop
» Pfam
» UniProt
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.

(click anywhere in this window to remove it)
» XML File
» XML Schema
» Coordinates (PDB)
» apo binding site (PDB)
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.

(click anywhere in this window to remove it)
pdb ID Ligand Unique ID #atoms #contacts
2hub EDOB1001 EPEB2001 19 75 Details
1yik MM1B_500 MM1B_501 30 86 Details
1sf6 NAGB_201 NAGB_203 NAGB_204 NAGB_202 57 172 Details
1lzc NAGA_130 NAGA_133 NAGA_131 NAGA_132 57 150 Details
NAGB_130 NAGB_131 NAGB_133 NAGB_132 57 152
1jj0 SUCC2380 23 70 Details
SUCD2380 23 74
1sfb NAGB_201 NAGB_205 NAGB_203 NAGB_204 NAGB_202 71 190 Details
1hew NAGB_201 NAGB_203 NAGB_202 43 115 Details
NAGA_201 NAGA_202 NAGA_203 43 116
1uih NAGB_501 NAGB_503 NAGB_502 43 107 Details
NAGA_501 NAGA_502 NAGA_503 43 112
1at5 NAGB_130 NAGB_131 NAGB_132 43 88 Details
NAGA_130 NAGA_132 NAGA_131 43 84
1lzb NAGB_130 NAGB_131 NAGB_132 43 111 Details
NAGA_130 NAGA_132 NAGA_131 43 109
1sf7 NAGB_201 NAGB_203 NAGB_204 NAGB_202 57 167 Details
1uc0 GALB_130 NAGB_131 GOLB_132 30 98 Details
1sfg NAGB_201 NAGB_205 NAGB_203 NAGB_204 NAGB_206 NAGB_202 85 198 Details
1yil MM2B_500 MM2B_501 30 90 Details
1sf4 NAGB_201 NAGB_202 29 104 Details
v4.0
May 2008		 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
Script execution time: 0.0882 seconds