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), 0.236 (DCC)
R-Value Work:
0.209 (Depositor), 0.209 (DCC)
R-Value Observed:
0.211 (Depositor)

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
Modeled Residue Count: 837
Deposited Residue Count: 960
Unique protein chains: 1

Macromolecules

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| 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 (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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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] mmCIF format, chain C [auth A] mmCIF 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] mmCIF format, chain E [auth A] mmCIF 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] mmCIF format, chain D [auth A] mmCIF 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 (Depositor), 0.236 (DCC)
R-Value Work: 0.209 (Depositor), 0.209 (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

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Ligand Structure Quality Assessment

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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