8RUT | pdb_00008rut

HIF prolyl-hydroxylase-2 (PHD2) T387V variant bound to Fe(III), 2-oxoglutarate (2OG) and Hypoxia-inducible Factor-2alpha (HIF-2alpha)

  • Classification: OXIDOREDUCTASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): Yes 

  • Deposited: 2024-01-31 Released: 2025-02-12 
  • Deposition Author(s): Fiorini, G., Schofield, C.J.
  • Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC), Cancer Research UK, Wellcome Trust, Other government

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 
    0.219 (Depositor), 0.216 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.192 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history. 


Literature

HIF prolyl hydroxylase 2 (PHD2) T387V variant bound to Hypoxia-inducible Factor 2alpha (HIF-2alpha

Fiorini, G., Schofield, C.J.

To be published.

Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Egl nine homolog 1227Homo sapiensMutation(s): 1 
Gene Names: EGLN1, C1orf12, PNAS-118, PNAS-137
EC: 1.14.11.29
UniProt & NIH Common Fund Data Resources
Find proteins for Q9GZT9 (Homo sapiens)
Explore Q9GZT9 
Go to UniProtKB:  Q9GZT9
PHAROS:  Q9GZT9
GTEx:  ENSG00000135766 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9GZT9
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Hypoxia-inducible Factor-2alpha20Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q99814 (Homo sapiens)
Explore Q99814 
Go to UniProtKB:  Q99814
PHAROS:  Q99814
GTEx:  ENSG00000116016 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99814
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free:  0.219 (Depositor), 0.216 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.192 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.24α = 90
b = 38.34β = 90
c = 42.98γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
xia2data reduction
d*TREKdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/R013829/1, BB/J001694/2, BB/L000121/1
Cancer Research UKUnited KingdomC8717/A18245
Wellcome TrustUnited Kingdom091857/7/10/7
Other governmentNewton Abraham Scholarship

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-12
    Type: Initial release