4KBZ | pdb_00004kbz

Crystal Structure of Hypoxia-Inducible Factor Prolyl Hydroxylase (PHD2) with (S)-{2-[2-(5-Cyano-3-hydroxy-pyridin-2-yl)-thiazol-4-yl]-acetylamino}-phenyl-acetic acid

• PDB DOI: https://doi.org/10.2210/pdb4KBZ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2013-04-24 Released: 2013-05-15 
• Deposition Author(s): Kim, H.T., Hong, Y.R., Chang, H.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.230 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.224 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Starting Model: experimental

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 27.42 kDa 
• Atom Count: 1,920 
• Modeled Residue Count: 231 
• Deposited Residue Count: 238 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Egl nine homolog 1	A	238	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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1QA	B [auth A]	(2S)-({[2-(5-cyano-3-hydroxypyridin-2-yl)-1,3-thiazol-4-yl]acetyl}amino)(phenyl)ethanoic acid C19 H14 N4 O4 S KPGRSPXHOOAVBE-INIZCTEOSA-N
SO4	D [auth A], E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
FE2	C [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.230 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.224 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.207	α = 90
b = 72.207	β = 90
c = 46.01	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASES	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-15 
Deposition Author(s): Kim, H.T., Hong, Y.R., Chang, H.J.

Revision History  

• Version 1.0: 2013-05-15
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description