2Y33

S-nitrosylated PHD2 (GSNO soaked) in complex with Zn(II) and UN9


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.209 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Studies on the Reaction of Nitric Oxide with the Hypoxia-Inducible Factor Prolyl Hydroxylase Domain 2 (Egln1)

Chowdhury, R.Flashman, E.Mecinovic, J.Kramer, H.B.Kessler, B.M.Frapart, Y.M.Boucher, J.-L.Clifton, I.J.McDonough, M.A.Schofield, C.J.

(2011) J Mol Biol 410: 268-279

  • DOI: https://doi.org/10.1016/j.jmb.2011.04.075
  • Primary Citation of Related Structures:  
    2Y33, 2Y34

  • PubMed Abstract: 

    The hypoxic response in animals is mediated via the transcription factor hypoxia-inducible factor (HIF). An oxygen-sensing component of the HIF system is provided by Fe(II) and 2-oxoglutarate-dependent oxygenases that catalyse the posttranslational hydroxylation of the HIF-α subunit. It is proposed that the activity of the HIF hydroxylases can be regulated by their reaction with nitric oxide. We describe biochemical and biophysical studies on the reaction of prolyl hydroxylase domain-containing enzyme (PHD) isoform 2 (EGLN1) with nitric oxide and a nitric oxide transfer reagent. The combined results reveal the potential for the catalytic domain of PHD2 to react with nitric oxide both at its Fe(II) and at cysteine residues. Although the biological significance is unclear, the results suggest that the reaction of PHD2 with nitric oxide has the potential to be complex and are consistent with proposals based on cellular studies that nitric oxide may regulate the hypoxic response by direct reaction with the HIF hydroxylases.


  • Organizational Affiliation

    Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
EGL NINE HOMOLOG 1252Homo sapiensMutation(s): 0 
EC: 1.14.11
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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UN9
Query on UN9

Download Ideal Coordinates CCD File 
C [auth A]N-[(1-CHLORO-4-HYDROXYISOQUINOLIN-3-YL)CARBONYL]GLYCINE
C12 H9 Cl N2 O4
OUQVKRKGTAUJQA-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SNC
Query on SNC
A
L-PEPTIDE LINKINGC3 H6 N2 O3 SCYS
Binding Affinity Annotations 
IDSourceBinding Affinity
UN9 BindingDB:  2Y33 Kd: 80 (nM) from 1 assay(s)
IC50: min: 70, max: 7500 (nM) from 8 assay(s)
EC50: 7.90e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.209 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.05α = 90
b = 111.05β = 90
c = 40.33γ = 120
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-12-29
    Type: Initial release
  • Version 1.1: 2011-06-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-03-28
    Changes: Database references
  • Version 1.4: 2019-01-30
    Changes: Data collection, Experimental preparation
  • Version 1.5: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description