4P8H | pdb_00004p8h

Crystal structure of M. tuberculosis DprE1 in complex with the nitro-benzothiazole 6a

• PDB DOI: https://doi.org/10.2210/pdb4P8H/pdb

• Classification: OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-03-31 Released: 2015-10-28 
• Deposition Author(s): Neres, J., Cole, S.T.
• Funding Organization(s): European Commission

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.307 (Depositor), 0.310 (DCC) 
• R-Value Work: 
  0.239 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.243 (Depositor) 

Literature

Non-mutagenic Nitrobenzothiazoles as Novel Anti-tubercular Agents: A Balance between Potency and Electron Affinity

Neres, J., Cole, S.T.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 107.18 kDa 
• Atom Count: 6,550 
• Modeled Residue Count: 829 
• Deposited Residue Count: 962 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable decaprenylphosphoryl-beta-D-ribose oxidase	A, B	481	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: dprE1, Rv3790, MT3898 EC: 1 (PDB Primary Data), 1.1.98.3 (UniProt)
UniProt
Find proteins for P9WJF1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WJF1  Go to UniProtKB:  P9WJF1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	C [auth A], E [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
O95	D [auth A], F [auth B]	{(4S)-2-[7-(hydroxyamino)-6-methyl-5-(trifluoromethyl)-1,3-benzothiazol-2-yl]-4,5-dihydro-1,3-oxazol-4-yl}(pyrrolidin-1-yl)methanone C17 H17 F3 N4 O3 S PDLYFURAMRBJFN-NSHDSACASA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.307 (Depositor), 0.310 (DCC) 
• R-Value Work:  0.239 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.243 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.045	α = 90
b = 77.297	β = 100.31
c = 81.209	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
PHASER	phasing
XDS	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-10-28 
Deposition Author(s): Neres, J., Cole, S.T.

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Funding Organization	Location	Grant Number
European Commission	Switzerland	260872

Revision History  

• Version 1.0: 2015-10-28
  Type: Initial release
  
• Version 1.1: 2023-12-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.2: 2024-10-30
  Changes: Structure summary