8RUZ | pdb_00008ruz

Anaerobic HIF prolyl-hydroxylase-2 (PHD2) T387S variant bound to acetate (ACT) 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: 1.82 Å
  • R-Value Free: 
    0.314 (Depositor), 0.312 (DCC) 
  • R-Value Work: 
    0.263 (Depositor), 0.263 (DCC) 
  • R-Value Observed: 
    0.266 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8RUZ

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

Literature

Investigating gatekeeper residues in Prolyl hydroxyalse 2

Fiorini, G., Schofield, C.J.

To be published.

Macromolecule Content 

  • Total Structure Weight: 27.69 kDa 
  • Atom Count: 1,948 
  • Modeled Residue Count: 238 
  • Deposited Residue Count: 246 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:
|  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-2alpha19Homo 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
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ACT

Query on ACT


Download:Ideal Coordinates CCD File
C [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free:  0.314 (Depositor), 0.312 (DCC) 
  • R-Value Work:  0.263 (Depositor), 0.263 (DCC) 
  • R-Value Observed: 0.266 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.295α = 90
b = 37.951β = 90
c = 42.076γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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