7DUD | pdb_00007dud

Crystal Structure of erWalK


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 
    0.248 (Depositor), 0.249 (DCC) 
  • R-Value Work: 
    0.225 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 
    0.226 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Asymmetric total synthesis of polycyclic xanthenes and discovery of a WalK activator active against MRSA.

Cheng, M.J.Wu, Y.Y.Zeng, H.Zhang, T.H.Hu, Y.X.Liu, S.Y.Cui, R.Q.Hu, C.X.Zou, Q.M.Li, C.C.Ye, W.C.Huang, W.Wang, L.

(2024) Nat Commun 15: 5879-5879

  • DOI: https://doi.org/10.1038/s41467-024-49629-8
  • Primary Citation Related Structures: 
    7DUD

  • PubMed Abstract: 

    The development of new antibiotics continues to pose challenges, particularly considering the growing threat of multidrug-resistant Staphylococcus aureus. Structurally diverse natural products provide a promising source of antibiotics. Herein, we outline a concise approach for the collective asymmetric total synthesis of polycyclic xanthene myrtucommulone D and five related congeners. The strategy involves rapid assembly of the challenging benzopyrano[2,3-a]xanthene core, highly diastereoselective establishment of three contiguous stereocenters through a retro-hemiketalization/double Michael cascade reaction, and a Mitsunobu-mediated chiral resolution approach with high optical purity and broad substrate scope. Quantum mechanical calculations provide insight into stereoselective construction mechanism of the three contiguous stereocenters. Additionally, this work leads to the discovery of an antibacterial agent against both drug-sensitive and drug-resistant S. aureus. This compound operates through a unique mechanism that promotes bacterial autolysis by activating the two-component sensory histidine kinase WalK. Our research holds potential for future antibacterial drug development.


  • Organizational Affiliation
    • State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou, 510632, P. R. China.

Macromolecule Content 

  • Total Structure Weight: 34.17 kDa 
  • Atom Count: 2,569 
  • Modeled Residue Count: 294 
  • Deposited Residue Count: 298 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Sensor protein kinase WalK
A, B
149Staphylococcus aureusMutation(s): 0 
Gene Names: walKSAMEA103891408_00013SAMEA103891434_00037
EC: 2.7.13.3
UniProt
Find proteins for Q2G2U4 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2G2U4 
Go to UniProtKB:  Q2G2U4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2G2U4
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.248 (Depositor), 0.249 (DCC) 
  • R-Value Work:  0.225 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 0.226 (Depositor) 
Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.63α = 90
b = 66.63β = 90
c = 80.083γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2022-01-19 
  • Deposition Author(s): Huang, W.

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-19
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description
  • Version 1.2: 2026-06-03
    Changes: Database references, Structure summary