4JAA | pdb_00004jaa

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

• PDB DOI: https://doi.org/10.2210/pdb4JAA/pdb

• Classification: OXIDOREDUCTASE/PEPTIDE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-02-18 Released: 2014-02-19 
• Deposition Author(s): Scotti, J.S., Ge, W., McDonough, M.A., Schofield, C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 
  0.219 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

Structure of an oxygenase in complex with substrate

Scotti, J.S., Ge, W., McDonough, M.A., 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 PISA (software)

Macromolecule Content 

• Total Structure Weight: 42.96 kDa 
• Atom Count: 2,909 
• Modeled Residue Count: 344 
• Deposited Residue Count: 369 
• 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
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)LEU	B [auth S]	20	N/A	Mutation(s): 0

Small Molecules

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

Binding Affinity Annotations
ID	Source	Binding Affinity
OGA	BindingDB:  4JAA	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: 2.39 Å
• R-Value Free:  0.219 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.079	α = 90
b = 86.079	β = 90
c = 147.029	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
GDA	data collection
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-02-19 
Deposition Author(s): Scotti, J.S., Ge, W., McDonough, M.A., Schofield, C.J.

Revision History  

• Version 1.0: 2014-02-19
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-10-30
  Changes: Structure summary