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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1wxf
LIGASE HEADER
E.COLI NAD SYNTHETASE TITLE
NH(3)-DEPENDENT NAD(+) SYNTHETASE 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 TYR
37 TYR
39 PHE
40 ILE
45 LEU
46 GLY
47 ILE
48 SER
50 GLY
51 GLN
52 ASP
53 SER
81 VAL
82 ARG
83 LEU
84 PRO
88 GLN
132 PHE
135 GLY
136 ASN
139 ALA
140 ARG
142 ARG
146 GLN
147 TYR
150 ALA
151 GLY
155 GLY
156 VAL
160 THR
165 GLU
169 GLY
170 PHE
171 PHE
172 THR
173 LYS
176 ASP
180 ASP
181 ILE
189 LYS
223 ASP
225 VAL
226 ALA
227 LEU
231 TYR
254 TRP
257 LYS
258 THR
260 HIS
261 LYS
266 ILE
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
1wxg DNDF_300 44 159 Details
DNDC_300 44 161
1wxi AMPL_400 DPOK_500 _MGI_600 _MGJ_700 34 110 Details
AMPF_400 _MGC_600 _MGD_700 DPOE_500 34 107
AMPB_300 23 96
AMPH_300 23 94
1wxe AMPB_500 23 102 Details
AMPH_400 _MGG_300 24 87
AMPF_500 23 98
AMPD_400 _MGC_300 24 87
1wxh NADB_400 44 158 Details
NADD_400 44 154
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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