3Q5R

Crystal structure of BmrR bound to Kanamycin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural contributions to multidrug recognition in the multidrug resistance (MDR) gene regulator, BmrR.

Bachas, S.Eginton, C.Gunio, D.Wade, H.

(2011) Proc.Natl.Acad.Sci.USA 108: 11046-11051

  • DOI: 10.1073/pnas.1104850108
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Current views of multidrug (MD) recognition focus on large drug-binding cavities with flexible elements. However, MD recognition in BmrR is supported by a small, rigid drug-binding pocket. Here, a detailed description of MD binding by the noncanonica ...

    Current views of multidrug (MD) recognition focus on large drug-binding cavities with flexible elements. However, MD recognition in BmrR is supported by a small, rigid drug-binding pocket. Here, a detailed description of MD binding by the noncanonical BmrR protein is offered through the combined use of X-ray and solution studies. Low shape complementarity, suboptimal packing, and efficient burial of a diverse set of ligands is facilitated by an aromatic docking platform formed by a set of conformationally fixed aromatic residues, hydrophobic pincer pair that locks the different drug structures on the adaptable platform surface, and a trio of acidic residues that enables cation selectivity without much regard to ligand structure. Within the binding pocket is a set of BmrR-derived H-bonding donor and acceptors that solvate a wide range of ligand polar substituent arrangements in a manner analogous to aqueous solvent. Energetic analyses of MD binding by BmrR are consistent with structural data. A common binding orientation for the different BmrR ligands is in line with promiscuous allosteric regulation.


    Organizational Affiliation

    Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Multidrug-efflux transporter 1 regulator
A
284Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: bmrR (bmr1R)
Find proteins for P39075 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P39075
Entity ID: 2
MoleculeChainsLengthOrganism
23 bp promoter DNAB23N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KAN
Query on KAN

Download SDF File 
Download CCD File 
A
KANAMYCIN A
C18 H36 N4 O11
SBUJHOSQTJFQJX-NOAMYHISSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.211 
  • Space Group: P 43 2 2
Unit Cell:
Length (Å)Angle (°)
a = 106.891α = 90.00
b = 106.891β = 90.00
c = 145.774γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
MAR345dtbdata collection
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-07-20
    Type: Initial release
  • Version 1.1: 2017-11-08
    Type: Refinement description, Structure summary