9LG0 | pdb_00009lg0

Crystal Structure of Human Peroxiredoxin I in Complex with SAB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 
    0.189 (Depositor), 0.191 (DCC) 
  • R-Value Work: 
    0.162 (Depositor), 0.163 (DCC) 
  • R-Value Observed: 
    0.164 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Augmentation of PRDX1-DOK3 interaction alleviates rheumatoid arthritis progression by suppressing plasma cell differentiation.

Dang, W.Wang, X.Li, H.Xu, Y.Li, X.Huang, S.Tao, H.Li, X.Yang, Y.Xuan, L.Xiao, W.Guo, D.Zhang, H.Wu, Q.Zheng, J.Shen, X.Chen, K.Xu, H.Zhang, Y.Luo, C.

(2025) Acta Pharm Sin B 15: 3997-4013

  • DOI: https://doi.org/10.1016/j.apsb.2025.06.006
  • Primary Citation of Related Structures:  
    9LG0

  • PubMed Abstract: 

    Rheumatoid arthritis (RA) is a chronic autoimmune disease characterized by persistent inflammation and joint damage, accompanied by the accumulation of plasma cells, which contributes to its pathogenesis. Understanding the genetic alterations occurring during plasma cell differentiation in RA can deepen our comprehension of its pathogenesis and guide the development of targeted therapeutic interventions. Here, our study elucidates the intricate molecular mechanisms underlying plasma cell differentiation by demonstrating that PRDX1 interacts with DOK3 and modulates its degradation by the autophagy-lysosome pathway. This interaction results in the inhibition of plasma cell differentiation, thereby alleviating the progression of collagen-induced arthritis. Additionally, our investigation identifies Salvianolic acid B (SAB) as a potent small molecular glue-like compound that enhances the interaction between PRDX1 and DOK3, consequently impeding the progression of collagen-induced arthritis by inhibiting plasma cell differentiation. Collectively, these findings underscore the therapeutic potential of developing chemical stabilizers for the PRDX1-DOK3 complex in suppressing plasma cell differentiation for RA treatment and establish a theoretical basis for targeting PRDX1-protein interactions as specific therapeutic targets in various diseases.


  • Organizational Affiliation
    • School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxiredoxin-1
A, B
175Homo sapiensMutation(s): 2 
Gene Names: PRDX1PAGAPAGBTDPX2
EC: 1.11.1.24
UniProt & NIH Common Fund Data Resources
Find proteins for Q06830 (Homo sapiens)
Explore Q06830 
Go to UniProtKB:  Q06830
PHAROS:  Q06830
GTEx:  ENSG00000117450 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06830
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1LXC (Subject of Investigation/LOI)
Query on A1LXC

Download Ideal Coordinates CCD File 
C [auth A]Salvianolic Acid B
C36 H32 O16
JUFYZLWTPPZFMH-MZBUKOFNSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free:  0.189 (Depositor), 0.191 (DCC) 
  • R-Value Work:  0.162 (Depositor), 0.163 (DCC) 
  • R-Value Observed: 0.164 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.793α = 90
b = 78.37β = 90
c = 82.149γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2025-10-01 
  • Deposition Author(s): Xu, H., Luo, C.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)ChinaU23A20108

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-01
    Type: Initial release
  • Version 2.0: 2025-11-19
    Changes: Data collection, Derived calculations, Non-polymer description, Structure summary