6LI6 | pdb_00006li6

Crystal structure of MCR-1-S treated by Au(PEt3)Cl


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 
    0.210 (Depositor), 0.214 (DCC) 
  • R-Value Work: 
    0.179 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 
    0.180 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Resensitizing carbapenem- and colistin-resistant bacteria to antibiotics using auranofin.

Sun, H.Zhang, Q.Wang, R.Wang, H.Wong, Y.T.Wang, M.Hao, Q.Yan, A.Kao, R.Y.Ho, P.L.Li, H.

(2020) Nat Commun 11: 5263-5263

  • DOI: https://doi.org/10.1038/s41467-020-18939-y
  • Primary Citation Related Structures: 
    6LHE, 6LI4, 6LI5, 6LI6

  • PubMed Abstract: 

    Global emergence of Gram-negative bacteria carrying the plasmid-borne resistance genes, bla MBL and mcr, raises a significant challenge to the treatment of life-threatening infections by the antibiotics, carbapenem and colistin (COL). Here, we identify an antirheumatic drug, auranofin (AUR) as a dual inhibitor of metallo-β-lactamases (MBLs) and mobilized colistin resistance (MCRs), two resistance enzymes that have distinct structures and substrates. We demonstrate that AUR irreversibly abrogates both enzyme activity via the displacement of Zn(II) cofactors from their active sites. We further show that AUR synergizes with antibiotics on killing a broad spectrum of carbapenem and/or COL resistant bacterial strains, and slows down the development of β-lactam and COL resistance. Combination of AUR and COL rescues all mice infected by Escherichia coli co-expressing MCR-1 and New Delhi metallo-β-lactamase 5 (NDM-5). Our findings provide potential therapeutic strategy to combine AUR with antibiotics for combating superbugs co-producing MBLs and MCRs.


  • Organizational Affiliation
    • Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, China. hsun@hku.hk.

Macromolecule Content 

  • Total Structure Weight: 75.68 kDa 
  • Atom Count: 5,323 
  • Modeled Residue Count: 646 
  • Deposited Residue Count: 672 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Probable phosphatidylethanolamine transferase Mcr-1
A, B
336Escherichia coliMutation(s): 0 
Gene Names: mcr1mcr-1APZ14_31440
EC: 2.7 (PDB Primary Data), 2.7.8.43 (UniProt)
UniProt
Find proteins for A0A0R6L508 (Escherichia coli)
Explore A0A0R6L508 
Go to UniProtKB:  A0A0R6L508
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0R6L508
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TPO
Query on TPO
A, B
L-PEPTIDE LINKINGC4 H10 N O6 PTHR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free:  0.210 (Depositor), 0.214 (DCC) 
  • R-Value Work:  0.179 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 0.180 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.82α = 90
b = 84.75β = 98.17
c = 81.6γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-16
    Type: Initial release
  • Version 1.1: 2020-10-28
    Changes: Database references
  • Version 1.2: 2024-10-16
    Changes: Data collection, Database references, Structure summary