4PFD | pdb_00004pfd

Crystal structure of M. tuberculosis in complex with a cBT - non-covalent adduct

• PDB DOI: https://doi.org/10.2210/pdb4PFD/pdb

• Classification: oxidoreductase/oxidoreductase inhibitor
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-04-28 Released: 2015-10-21 
• Deposition Author(s): Neres, J., Panda, M., Cole, S.
• Funding Organization(s): European Commission

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.236 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Literature

Crystal structure of M. tuberculosis in complex with a cBT

Neres, J., Cole, S.

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: 107.09 kDa 
• Atom Count: 6,779 
• Modeled Residue Count: 837 
• Deposited Residue Count: 960 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable decaprenylphosphoryl-beta-D-ribose oxidase	A, B	480	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: dprE1, Rv3790 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	C [auth A], F [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
2R2	E [auth A], G [auth B]	[4-(2-methoxyethyl)piperazin-1-yl][6-methyl-7-nitro-5-(trifluoromethyl)-1,3-benzothiazol-2-yl]methanone C17 H19 F3 N4 O4 S AOMUWGOWJLARPE-UHFFFAOYSA-N
IMD	D [auth A], H [auth B]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.236 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.521	α = 90
b = 84.129	β = 100.73
c = 90.149	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
PHASER	phasing
REFMAC	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-10-21 
Deposition Author(s): Neres, J., Panda, M., Cole, S.

---

Funding Organization	Location	Grant Number
European Commission		MM4TB - 260872

Revision History  

• Version 1.0: 2015-10-21
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Derived calculations, Refinement description
• Version 1.2: 2023-12-27
  Changes: Data collection, Database references