5KAW | pdb_00005kaw

The structure of SAV2435 bound to TETRAPHENYLPHOSPHONIUM and RHODAMINE 6G


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 
    0.194 (Depositor), 0.196 (DCC) 
  • R-Value Work: 
    0.165 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 
    0.167 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5KAW

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Solution Binding and Structural Analyses Reveal Potential Multidrug Resistance Functions for SAV2435 and CTR107 and Other GyrI-like Proteins.

Moreno, A.Froehlig, J.R.Bachas, S.Gunio, D.Alexander, T.Vanya, A.Wade, H.

(2016) Biochemistry 55: 4850-4863

  • DOI: https://doi.org/10.1021/acs.biochem.6b00651
  • Primary Citation Related Structures: 
    5KAT, 5KAU, 5KAV, 5KAW, 5KAX, 5KCB

  • PubMed Abstract: 

    Multidrug resistance (MDR) refers to the acquired ability of cells to tolerate a broad range of toxic compounds. One mechanism cells employ is to increase the level of expression of efflux pumps for the expulsion of xenobiotics. A key feature uniting efflux-related mechanisms is multidrug (MD) recognition, either by efflux pumps themselves or by their transcriptional regulators. However, models describing MD binding by MDR effectors are incomplete, underscoring the importance of studies focused on the recognition elements and key motifs that dictate polyspecific binding. One such motif is the GyrI-like domain, which is found in several MDR proteins and is postulated to have been adapted for small-molecule binding and signaling. Here we report the solution binding properties and crystal structures of two proteins containing GyrI-like domains, SAV2435 and CTR107, bound to various ligands. Furthermore, we provide a comparison with deposited crystal structures of GyrI-like proteins, revealing key features of GyrI-like domains that not only support polyspecific binding but also are conserved among GyrI-like domains. Together, our studies suggest that GyrI-like domains perform evolutionarily conserved functions connected to multidrug binding and highlight the utility of these types of studies for elucidating mechanisms of MDR.


  • Organizational Affiliation
    • Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine , 725 North Wolfe Street, Baltimore, Maryland 21205, United States.

Macromolecule Content 

  • Total Structure Weight: 20.08 kDa 
  • Atom Count: 1,499 
  • Modeled Residue Count: 165 
  • Deposited Residue Count: 165 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
SA2223 protein165Staphylococcus aureus subsp. aureus N315Mutation(s): 0 
Gene Names: SA2223

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RHQ

Query on RHQ



Download:Ideal Coordinates CCD File
B [auth A]RHODAMINE 6G
C28 H31 N2 O3
IWWWBRIIGAXLCJ-KRUMMXJUSA-O
P4P

Query on P4P



Download:Ideal Coordinates CCD File
C [auth A]TETRAPHENYLPHOSPHONIUM
C24 H20 P
USFPINLPPFWTJW-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free:  0.194 (Depositor), 0.196 (DCC) 
  • R-Value Work:  0.165 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 0.167 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.724α = 90
b = 73.724β = 90
c = 65.891γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesMCB-0953430
Arnold and Mabel Beckman Young Investigator AwardUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-24
    Type: Initial release
  • Version 1.1: 2016-09-07
    Changes: Database references
  • Version 1.2: 2019-11-27
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references