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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2ieb
OXIDOREDUCTASE HEADER
CRYSTAL STRUCTURE OF ISONIAZID-RESISTANT S94A ENOYL- ACP(COA) REDUCTASE MUTANT ENZYME FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH NADH-INH TITLE
ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH] 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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ZID F 300
14E GLY
15E ILE
16E ILE
17E THR
20E SER
21E ILE
22E ALA
40E GLY
41E PHE
63E LEU
64E ASP
65E VAL
66E GLN
93E HIS
94E ALA
95E ILE
96E GLY
97E PHE
122E ILE
147E MET
148E ASP
149E PHE
150E ASP
155E MET
158E TYR
161E MET
165E LYS
191E ALA
192E GLY
193E PRO
194E ILE
196E THR
198E ALA
199E MET
218E LEU
222E TRP
ZID D 300
14C GLY
15C ILE
16C ILE
17C THR
20C SER
21C ILE
22C ALA
40C GLY
41C PHE
63C LEU
64C ASP
65C VAL
66C GLN
93C HIS
94C ALA
95C ILE
96C GLY
97C PHE
122C ILE
147C MET
148C ASP
149C PHE
150C ASP
155C MET
158C TYR
161C MET
165C LYS
191C ALA
192C GLY
193C PRO
194C ILE
196C THR
198C ALA
199C MET
218C LEU
222C TRP
ZID B 300
14A GLY
15A ILE
16A ILE
17A THR
20A SER
21A ILE
22A ALA
40A GLY
41A PHE
63A LEU
64A ASP
65A VAL
66A GLN
93A HIS
94A ALA
95A ILE
96A GLY
97A PHE
122A ILE
147A MET
148A ASP
149A PHE
150A ASP
155A MET
158A TYR
161A MET
165A LYS
191A ALA
192A GLY
193A PRO
194A ILE
196A THR
198A ALA
199A MET
218A LEU
222A TRP
ZID H 300
14G GLY
15G ILE
16G ILE
17G THR
20G SER
21G ILE
22G ALA
40G GLY
41G PHE
63G LEU
64G ASP
65G VAL
66G GLN
93G HIS
94G ALA
95G ILE
96G GLY
97G PHE
122G ILE
147G MET
148G ASP
149G PHE
150G ASP
155G MET
158G TYR
161G MET
165G LYS
191G ALA
192G GLY
193G PRO
194G ILE
196G THR
198G ALA
199G MET
218G LEU
222G TRP
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
2ied 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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ZID NAME: ISONICOTINIC-ACETYL-NICOTINAMIDE-ADENINE DINUCLEOTIDE
FORMULA: C27 H30 N8 O15 P2
SMILES: NC(=O)c1c[n+](ccc1C(=O)c2ccncc2)C3OC(COP([O-])(=O)OP(O)(=O)OCC4OC(C(O)C4O)[n]5cnc6c(N)ncnc56)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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