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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1y3i
TRANSFERASE HEADER
CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS NAD KINASE- NAD COMPLEX TITLE
INORGANIC POLYPHOSPHATE/ATP-NAD KINASE 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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NAD K 501
12J HIS
85J ASP
86J GLY
89J LEU
109J ARG
110J ILE
111J GLY
112J PHE
113J LEU
159J ASN
160J GLU
164J GLU
165A LYS
169A LEU
170A GLY
171A VAL
189A ASP
197J THR
200J THR
201J ALA
202J TYR
205J SER
224A ASN
226A HIS
257J ASP
258J GLY
259J ARG
NAD B 501
12A HIS
85A ASP
86A GLY
89A LEU
109A ARG
110A ILE
111A GLY
112A PHE
113A LEU
159A ASN
160A GLU
164A GLU
165J LYS
169J LEU
170J GLY
171J VAL
189J ASP
197A THR
200A THR
201A ALA
202A TYR
205A SER
224J ASN
226J HIS
257A ASP
258A GLY
259A ARG
NAD P1501
85N ASP
86N GLY
89N LEU
109N ARG
110N ILE
111N GLY
112N PHE
113N LEU
159N ASN
160N GLU
165E LYS
169E LEU
170E GLY
171E VAL
189E ASP
197N THR
198N GLY
200N THR
201N ALA
202N TYR
205N SER
224E ASN
226E HIS
257N ASP
258N GLY
297N PHE
NAD G1501
85E ASP
86E GLY
89E LEU
109E ARG
110E ILE
111E GLY
112E PHE
113E LEU
159E ASN
160E GLU
165N LYS
169N LEU
170N GLY
171N VAL
189N ASP
197E THR
198E GLY
200E THR
201E ALA
202E TYR
205E SER
224N ASN
226N HIS
257E ASP
258E GLY
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
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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
1u0t Details
other holo-structures
pdb ID Ligand Unique ID
none
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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NAD NAME: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
FORMULA: C21 H27 N7 O14 P2
SMILES: NC(=O)c1ccc[n+](c1)C2OC(COP([O-])(=O)OP(O)(=O)OCC3OC(C(O)C3O)[n]4cnc5c(N)ncnc45)C(O)C2O
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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