4PFD

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
R-Value Work: 0.209
R-Value Observed: 0.211

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of M. tuberculosis in complex with a cBT

Neres, J., Cole, S.

To be published.

Macromolecule Content

Total Structure Weight: 107.09 kDa
Atom Count: 6,779
Modelled Residue Count: 837
Deposited Residue Count: 960
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
UniProt
Find proteins for P9WJF1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WJF1 Go to UniProtKB: P9WJF1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WJF1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B]	C [auth A], F [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
2R2 Query on 2R2 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B]	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		Interactions Focus chain E [auth A] Focus chain G [auth B] Interactions & Density Focus chain E [auth A] Focus chain G [auth B]
IMD Query on IMD Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B]	D [auth A], H [auth B]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.236
R-Value Work: 0.209
R-Value Observed: 0.211
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

View Full Validation Report

Ligand Structure Quality Assessment

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 (Full details and data files)

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

Prepare Data

Validate Data

Deposit Data

Help and Resources

4PFD

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

Crystal structure of M. tuberculosis in complex with a cBT

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)