1DFI

X-RAY STRUCTURE OF ESCHERICHIA COLI ENOYL REDUCTASE WITH BOUND NAD

PDB DOI: https://doi.org/10.2210/pdb1DFI/pdb

Classification: OXIDOREDUCTASE
Organism(s): Escherichia coli
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 1997-01-16 Released: 1998-01-28
Deposition Author(s): Baldock, C., Rafferty, J.B., Rice, D.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.09 Å
R-Value Work: 0.162

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

A mechanism of drug action revealed by structural studies of enoyl reductase.

Baldock, C., Rafferty, J.B., Sedelnikova, S.E., Baker, P.J., Stuitje, A.R., Slabas, A.R., Hawkes, T.R., Rice, D.W.

(1996) Science 274: 2107-2110

PubMed: 8953047 Search on PubMed
DOI: https://doi.org/10.1126/science.274.5295.2107
Primary Citation of Related Structures:
1DFG, 1DFH, 1DFI

PubMed Abstract:
Enoyl reductase (ENR), an enzyme involved in fatty acid biosynthesis, is the target for antibacterial diazaborines and the front-line antituberculosis drug isoniazid. Analysis of the structures of complexes of Escherichia coli ENR with nicotinamide adenine dinucleotide and either thienodiazaborine or benzodiazaborine revealed the formation of a covalent bond between the 2' hydroxyl of the nicotinamide ribose and a boron atom in the drugs to generate a tight, noncovalently bound bisubstrate analog. This analysis has implications for the structure-based design of inhibitors of ENR, and similarities to other oxidoreductases suggest that mimicking this molecular linkage may have generic applications in other areas of medicinal chemistry.

Organizational Affiliation

Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK. D.Rice@sheffield.ac.uk

Macromolecule Content

Total Structure Weight: 113.7 kDa
Atom Count: 7,839
Modelled Residue Count: 988
Deposited Residue Count: 1,044
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ENOYL ACYL CARRIER PROTEIN REDUCTASE	A, B, C, D	261	Escherichia coli	Mutation(s): 0 EC: 1.3.1.9
UniProt
Find proteins for P0AEK4 (Escherichia coli (strain K12)) Explore P0AEK4 Go to UniProtKB: P0AEK4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0AEK4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D]	E [auth A], F [auth B], G [auth C], H [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.09 Å
R-Value Work: 0.162
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74	α = 90
b = 81.2	β = 92.9
c = 79	γ = 90

Software Package:

Software Name	Purpose
CCP4	model building
TNT	refinement
MOSFLM	data reduction
Agrovata	data scaling
CCP4	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 1998-01-28

Deposition Author(s):

Baldock, C.

Rafferty, J.B.

Rice, D.W.

Revision History (Full details and data files)

Version 1.0: 1998-01-28
Type: Initial release
Version 1.1: 2008-03-24
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-08-09
Changes: Database references, Derived calculations, Other, Refinement description