9VI5 | pdb_00009vi5

The structure of coproporphyrin ferrochelatase(CpfC)in staphylococcus aureus.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 
    0.263 (Depositor), 0.258 (DCC) 
  • R-Value Work: 
    0.199 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 
    0.203 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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Literature

SHP-1 agonist SC-43 limits methicillin-resistant Staphylococcus aureus infection through inhibition of heme biosynthesis.

Huang, Y.Ye, Y.Zhu, X.Liang, D.Cui, R.Yuan, X.Li, X.Zou, Q.Li, H.Huang, W.

(2026) EMBO Mol Med 18: 1990-2005

  • DOI: https://doi.org/10.1038/s44321-026-00418-4
  • Primary Citation Related Structures: 
    9VI5

  • PubMed Abstract: 

    The limitations of existing drugs and the development of drug resistance make it urgent to develop new drugs against methicillin-resistant Staphylococcus aureus (MRSA). The re-development of the antibacterial activity of drugs that have already been proven safe for human use is an effective way. In this study, we discovered that the Src homology region 2 domain-containing phosphatase-1 (SHP-1) agonist SC-43, exhibits potent activity against Gram-positive bacteria, including MRSA. The mode of action studies revealed that SC-43 inhibits the key enzyme coproporphyrin ferrochelatase (CpfC) of the coproporphyrin-dependent (CPD) heme synthesis pathway and interferes with the bacterial porphyrin metabolism. The determination of the structure of CpfC derived from S. aureus (SA CpfC ) in this study allowed us to reveal the inhibitory effect of SC-43 at the molecular level. Animal experiments showed that SC-43 has the potential to become a new anti-MRSA drug. In conclusion, this study discovered a new anti-MRSA activity of a drug currently undergoing clinical trials and simultaneously verified the feasibility of developing new anti-Gram-positive bacteria drugs by inhibiting the CPD pathway.


  • Organizational Affiliation
    • Department of Laboratory Medicine, Shenzhen Key Laboratory of Pathogenic Microbiology and Antimicrobial Resistance Surveillance, Shenzhen People's Hospital, (The First Affiliated Hospital, Southern University of Science and Technology; The Second Clinical Medical College, Jinan University), Shenzhen, 518020, China.

Macromolecule Content 

  • Total Structure Weight: 69.58 kDa 
  • Atom Count: 5,160 
  • Modeled Residue Count: 608 
  • Deposited Residue Count: 608 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Coproporphyrin III ferrochelatase
A, B
304Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: cpfChemHSAOUHSC_01961
EC: 4.99.1.9
UniProt
Find proteins for Q2FXA4 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2FXA4 
Go to UniProtKB:  Q2FXA4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2FXA4
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free:  0.263 (Depositor), 0.258 (DCC) 
  • R-Value Work:  0.199 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 0.203 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.161α = 69.73
b = 54.45β = 84.85
c = 60.434γ = 90.07
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
autoPROCdata reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2026-05-06
    Type: Initial release
  • Version 1.1: 2026-05-27
    Changes: Database references