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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1kaq
TRANSFERASE HEADER
STRUCTURE OF BACILLUS SUBTILIS NICOTINIC ACID MONONUCLEOTIDE ADENYLYL TRANSFERASE TITLE
NICOTINATE-NUCLEOTIDE ADENYLYLTRANSFERASE 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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DND D 190
7C PHE
8C GLY
9C GLY
10C THR
11C PHE
15C HIS
17C GLY
18C HIS
21C MET
37C MET
39C ASN
76C GLU
83C SER
84C TYR
85C THR
103C PHE
104C ILE
105C ILE
106C GLY
107C ALA
108C ASP
109C MET
112C TYR
116C TRP
117C TYR
131C VAL
150C PRO
152C PHE
154C VAL
155C SER
DND B 201
7A PHE
8A GLY
9A GLY
10A THR
11A PHE
12A ASP
15A HIS
17A GLY
18A HIS
21A MET
37A MET
39A ASN
76A GLU
83A SER
84A TYR
85A THR
103A PHE
104A ILE
105A ILE
106A GLY
108A ASP
109A MET
112A TYR
116A TRP
117A TYR
131A VAL
133A ARG
134A PRO
152A PHE
154A VAL
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).

Clicking the blue 'Hide table of related structures' button removes the entire table.

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apo-structure
pdb ID
1kam 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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DND NAME: NICOTINIC ACID ADENINE DINUCLEOTIDE
FORMULA: C21 H27 N6 O15 P2
SMILES: Nc1ncnc2[n](cnc12)C3OC(COP(O)(=O)OP(O)(=O)OCC4OC(C(O)C4O)[n+]5cccc(c5)C(O)=O)C(O)C3O
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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