6HN3 | pdb_00006hn3

wildtype form (apo) of human GPX4 with Se-Cys46


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.01 Å
  • R-Value Free: 
    0.137 (Depositor), 0.152 (DCC) 
  • R-Value Work: 
    0.114 (Depositor) 
  • R-Value Observed: 
    0.115 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6HN3

This is version 2.1 of the entry. See complete history

Literature

Crystal structures of the selenoprotein glutathione peroxidase 4 in its apo form and in complex with the covalently bound inhibitor ML162.

Moosmayer, D.Hilpmann, A.Hoffmann, J.Schnirch, L.Zimmermann, K.Badock, V.Furst, L.Eaton, J.K.Viswanathan, V.S.Schreiber, S.L.Gradl, S.Hillig, R.C.

(2021) Acta Crystallogr D Struct Biol 77: 237-248

  • DOI: https://doi.org/10.1107/S2059798320016125
  • Primary Citation Related Structures: 
    6HKQ, 6HN3

  • PubMed Abstract: 

    Wild-type human glutathione peroxidase 4 (GPX4) was co-expressed with SBP2 (selenocysteine insertion sequence-binding protein 2) in human HEK cells to achieve efficient production of this selenocysteine-containing enzyme on a preparative scale for structural biology. The protein was purified and crystallized, and the crystal structure of the wild-type form of GPX4 was determined at 1.0 Å resolution. The overall fold and the active site are conserved compared with previously determined crystal structures of mutated forms of GPX4. A mass-spectrometry-based approach was developed to monitor the reaction of the active-site selenocysteine Sec46 with covalent inhibitors. This, together with the introduction of a surface mutant (Cys66Ser), enabled the crystal structure determination of GPX4 in complex with the covalent inhibitor ML162 [(S)-enantiomer]. The mass-spectrometry-based approach described here opens the path to further co-complex crystal structures of this potential cancer drug target in complex with covalent inhibitors.


  • Organizational Affiliation
    • Research and Development, Pharmaceuticals, Bayer AG, 13353 Berlin, Germany.

Macromolecule Content 

  • Total Structure Weight: 20.64 kDa 
  • Atom Count: 1,723 
  • Modeled Residue Count: 167 
  • Deposited Residue Count: 176 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Phospholipid hydroperoxide glutathione peroxidase176Homo sapiensMutation(s): 0 
Gene Names: GPX4
EC: 1.11.1.12 (PDB Primary Data), 1.11.1.9 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P36969 (Homo sapiens)
Explore P36969 
Go to UniProtKB:  P36969
PHAROS:  P36969
GTEx:  ENSG00000167468 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36969
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.01 Å
  • R-Value Free:  0.137 (Depositor), 0.152 (DCC) 
  • R-Value Work:  0.114 (Depositor) 
  • R-Value Observed: 0.115 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.76α = 103.18
b = 35.19β = 112.33
c = 37.82γ = 91.76
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-01
    Type: Initial release
  • Version 2.0: 2021-03-17
    Type: Coordinate replacement
    Reason: Model completeness
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary
  • Version 2.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description