4M4A

Human Hemoglobin Nitromethane Modified

• PDB DOI: https://doi.org/10.2210/pdb4M4A/pdb

• Classification: OXYGEN TRANSPORT
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2013-08-06 Released: 2014-07-16 
• Deposition Author(s): Yi, J., Guan, Y., Thomas, L.M., Richter-Addo, G.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.280 
• R-Value Work: 0.224 
• R-Value Observed: 0.227 

Starting Model: experimental

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

• PubMed: 24149619 
• DOI: https://doi.org/10.1039/c3cc46174b
• Primary Citation of Related Structures:  
  4M4A, 4M4B


• 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 to degrade Hb removing it from circulation.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA. [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Dihedral - D2  (Explore in 3D)
Pseudo Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 32.64 kDa 
• Atom Count: 2,434 
• Modelled Residue Count: 286 
• Deposited Residue Count: 287 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit alpha	A	141	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P69905 (Homo sapiens) Explore P69905  Go to UniProtKB:  P69905
PHAROS:  P69905 GTEx:  ENSG00000188536 ENSG00000206172

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit beta	B	146	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P68871 (Homo sapiens) Explore P68871  Go to UniProtKB:  P68871
PHAROS:  P68871 GTEx:  ENSG00000244734

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A], G [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
GOL	E [auth A], F [auth A], I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NSM	D [auth A], H [auth B]	NITROSOMETHANE C H3 N O IMHRONYAKYWGCC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.280 
• R-Value Work: 0.224 
• R-Value Observed: 0.227 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.573	α = 90
b = 53.573	β = 90
c = 191.87	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
PHENIX	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-07-16 
Deposition Author(s): Yi, J., Guan, Y., Thomas, L.M., Richter-Addo, G.B.

Revision History  

• Version 1.0: 2014-07-16
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description