8RUV | pdb_00008ruv

HIF prolyl hydroxylase 2 (PHD2) T387I variant bound to Fe(III), 2-oxoglutarate (2OG) and Hypoxia-inducible Factor 2alpha (HIF2alpha)

• PDB DOI: https://doi.org/10.2210/pdb8RUV/pdb

• 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., Arif, F., Kibria, M.M.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC), Cancer Research UK, Wellcome Trust, Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free: 
  0.257 (Depositor), 0.257 (DCC) 
• R-Value Work: 
  0.238 (Depositor), 0.239 (DCC) 
• R-Value Observed: 
  0.239 (Depositor) 

Starting Model: experimental

Literature

Investigating gatekeeper residues in Prolyl hydroxylase 2

Fiorini, G., Schofield, C.J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by (software)

Macromolecule Content 

• Total Structure Weight: 27.86 kDa 
• Atom Count: 2,027 
• Modeled Residue Count: 237 
• Deposited Residue Count: 246 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Egl nine homolog 1	A	227	Homo sapiens	Mutation(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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypoxia-inducible Factor-2alpha	B	19	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q99814 (Homo sapiens) Explore Q99814  Go to UniProtKB:  Q99814
PHAROS:  Q99814 GTEx:  ENSG00000116016

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AKG (Subject of Investigation/LOI)	D [auth A]	2-OXOGLUTARIC ACID C5 H6 O5 KPGXRSRHYNQIFN-UHFFFAOYSA-N
FE (Subject of Investigation/LOI)	C [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free:  0.257 (Depositor), 0.257 (DCC) 
• R-Value Work:  0.238 (Depositor), 0.239 (DCC) 
• R-Value Observed: 0.239 (Depositor) 

Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.116	α = 90
b = 42.956	β = 90
c = 130.508	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
xia2	data reduction
DIALS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-02-12 
Deposition Author(s): Fiorini, G., Schofield, C.J., Arif, F., Kibria, M.M.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/R013829/1, BB/J001694/2, BB/L000121/1
Cancer Research UK	United Kingdom	C8717/A18245
Wellcome Trust	United Kingdom	091857/7/10/7
Other government		Newton Abraham Scholarship

Revision History  

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