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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1wxi
LIGASE HEADER
E.COLI NAD SYNTHETASE, AMP.PP TITLE
NH(3)-DEPENDENT NAD(+) SYNTHETASE 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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AMP B 300
33G TYR
37G TYR
39G PHE
40G ILE
132A PHE
136A ASN
140A ARG
147G TYR
150G ALA
151G GLY
155G GLY
156G VAL
171A PHE
172A THR
173A LYS
180G ASP
181G ILE
257A LYS
260A HIS
261A LYS
266A ILE
AMP H 300
33A TYR
37A TYR
39A PHE
40A ILE
132G PHE
136G ASN
140G ARG
147A TYR
150A ALA
151A GLY
155A GLY
156A VAL
172G THR
173G LYS
180A ASP
181A ILE
257G LYS
260G HIS
261G LYS
266G ILE
AMP L 400
45G LEU
46G GLY
47G ILE
48G SER
53G SER
81G VAL
82G ARG
83G LEU
88G GLN
142G ARG
146G GLN
160G THR
165G GLU
170G PHE
171G PHE
176G ASP
223G ASP
AMP F 400
45A LEU
46A GLY
47A ILE
48A SER
53A SER
81A VAL
82A ARG
83A LEU
88A GLN
142A ARG
146A GLN
160A THR
165A GLU
170A PHE
176A ASP
223A ASP
DPO K 500
48G SER
50G GLY
51G GLN
52G ASP
53G SER
165G GLU
189G LYS
223G ASP
MG J 700
48G SER
MG D 700
48A SER
DPO E 500
48A SER
50A GLY
51A GLN
52A ASP
53A SER
165A GLU
189A LYS
223A ASP
MG I 600
52G ASP
160G THR
165G GLU
MG C 600
52A ASP
160A THR
165A GLU
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).

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apo-structure
pdb ID
1wxf Details
other holo-structures
pdb ID Ligand Unique ID
1wxg DNDF_300 Details
DNDC_300
1wxe AMPB_500 Details
AMPH_400 _MGG_300
AMPF_500
AMPD_400 _MGC_300
1wxh NADB_400 Details
NADD_400
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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AMP NAME: ADENOSINE MONOPHOSPHATE
FORMULA: C10 H14 N5 O7 P1
SMILES: Nc1ncnc2[n](cnc12)C3OC(COP(O)(O)=O)C(O)C3O
DPO NAME: DIPHOSPHATE
FORMULA: O7 P2
SMILES: [O-]P([O-])(=O)OP([O-])([O-])=O
MG NAME: MAGNESIUM ION
FORMULA: MG1
SMILES: [Mg++]
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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