3Q3S | pdb_00003q3s

EthR from Mycobacterium tuberculosis in complex with compound BDM5683

PDB DOI: https://doi.org/10.2210/pdb3Q3S/pdb

Classification: TRANSCRIPTION REPRESSOR/INHIBITOR
Organism(s): Mycobacterium tuberculosis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-12-22 Released: 2012-01-18
Deposition Author(s): Lens, Z., Willand, N., Villeret, V.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.232 (Depositor), 0.230 (DCC)
R-Value Work:
0.189 (Depositor), 0.190 (DCC)
R-Value Observed:
0.191 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

EthR from Mycobacterium tuberculosis in complex with compound BDM5683

Willand, N., Lens, Z., Villeret, V.

To be published.

Macromolecule Content

Total Structure Weight: 26.33 kDa
Atom Count: 1,706
Modelled Residue Count: 194
Deposited Residue Count: 236
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HTH-type transcriptional regulator EthR	A	236	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: ethR, etaR, MT3970, Rv3855
UniProt
Find proteins for P9WMC1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WMC1 Go to UniProtKB: P9WMC1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WMC1
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
O8B Query on O8B Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	2-(2-methylphenoxy)-N-[2-(4-methylphenyl)-2H-benzotriazol-5-yl]acetamide C₂₂ H₂₀ N₄ O₂ LKAZLKLHUAIYCE-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
O8B	BindingDB: 3Q3S	EC50: 1.00e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.232 (Depositor), 0.230 (DCC)
R-Value Work: 0.189 (Depositor), 0.190 (DCC)
R-Value Observed: 0.191 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.16	α = 90
b = 121.16	β = 90
c = 33.82	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-01-18

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-01-18
Type: Initial release
Version 1.1: 2024-02-21
Changes: Data collection, Database references, Derived calculations

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.