4M4A

Human Hemoglobin Nitromethane Modified


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Degradation of human hemoglobin by organic C-nitroso compounds.

Yi, J.Ye, G.Thomas, L.M.Richter-Addo, G.B.

(2013) Chem.Commun.(Camb.) 49: 11179-11181

  • DOI: 10.1039/c3cc46174b
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The crystal structure of the nitrosomethane adduct of human Hb shows N-binding of the MeNO ligands to heme Fe. The structure of the EtNO adduct reveals a surprising 4.9 Å heme slippage in the β subunit, and explains the ability of C-nitroso compounds ...

    The crystal structure of the nitrosomethane adduct of human Hb shows N-binding of the MeNO ligands to heme Fe. The structure of the EtNO adduct reveals a surprising 4.9 Å heme slippage in the β subunit, and explains the ability of C-nitroso compounds to degrade Hb removing it from circulation.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA. yijun@ou.edu grichteraddo@ou.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemoglobin subunit alpha
A
141Homo sapiensGene Names: HBA1, HBA2
Find proteins for P69905 (Homo sapiens)
Go to Gene View: HBA1 HBA2
Go to UniProtKB:  P69905
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hemoglobin subunit beta
B
146Homo sapiensGene Names: HBB
Find proteins for P68871 (Homo sapiens)
Go to Gene View: HBB
Go to UniProtKB:  P68871
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NSM
Query on NSM

Download SDF File 
Download CCD File 
A, B
NITROSOMETHANE
C H3 N O
IMHRONYAKYWGCC-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.224 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 53.573α = 90.00
b = 53.573β = 90.00
c = 191.870γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
d*TREKdata scaling
d*TREKdata reduction
PHASERphasing
CrystalCleardata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-16
    Type: Initial release