6RUJ | pdb_00006ruj

Factor inhibiting HIF-1 alpha in complex with consensus ankyrin repeat domain-(d)3-hydroxy-Leu peptide

• PDB DOI: https://doi.org/10.2210/pdb6RUJ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-05-28 Released: 2020-07-08 
• Deposition Author(s): Nakashima, Y., McDonough, M.A., Schofield, C.J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.42 Å
• R-Value Free: 
  0.257 (Depositor), 0.264 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Starting Model: experimental

Literature

A human protein hydroxylase that accepts D-residues

Choi, H., Hardy, A., Leissing, T.M., Chowdhury, R., Ge, W., Markoulides, M., Scotti, J.S., Thorbjornsrud, H., Nakashima, Y., Kang, D., Hong, S., Lee, J., Park, H., McDonough, M.A., Schofield, C.J.

(2020) Commun Chem 

• DOI: https://doi.org/10.1038/s42004-020-0290-5

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 42.45 kDa 
• Atom Count: 2,994 
• Modeled Residue Count: 364 
• Deposited Residue Count: 364 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypoxia-inducible factor 1-alpha inhibitor	A	349	Homo sapiens	Mutation(s): 0  Gene Names: HIF1AN, FIH1 EC: 1.14.11.30 (PDB Primary Data), 1.14.11 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NWT6 (Homo sapiens) Explore Q9NWT6  Go to UniProtKB:  Q9NWT6
PHAROS:  Q9NWT6 GTEx:  ENSG00000166135

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CONSENSUS ANKYRIN REPEAT DOMAIN-(D)3-hydroxy-Leu	B	15	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OGA (Subject of Investigation/LOI)	D [auth A]	N-OXALYLGLYCINE C4 H5 N O5 BIMZLRFONYSTPT-UHFFFAOYSA-N
SO4	E [auth A], F [auth A], G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN (Subject of Investigation/LOI)	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
OGA	BindingDB:  6RUJ	Ki: 1.20e+6 (nM) from 1 assay(s)
		IC50: 4.60e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.42 Å
• R-Value Free:  0.257 (Depositor), 0.264 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.401	α = 90
b = 86.401	β = 90
c = 147.263	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-07-08 
Deposition Author(s): Nakashima, Y., McDonough, M.A., Schofield, C.J.

Revision History  

• Version 1.0: 2020-07-08
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description