4M4A | pdb_00004m4a

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.280 (Depositor), 0.280 (DCC)
R-Value Work:
0.224 (Depositor), 0.223 (DCC)
R-Value Observed:
0.227 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 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

PubMed: 24149619 Search on PubMed
DOI: https://doi.org/10.1039/c3cc46174b
Primary Citation 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.

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P69905
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P68871
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain C [auth A] MOL2 format, chain G [auth B] MOL2 format, chain C [auth A] mmCIF format, chain G [auth B] mmCIF format, chain C [auth A]	C [auth A], G [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B]	E [auth A], F [auth A], I [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B]
NSM Query on NSM Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain D [auth A]	D [auth A], H [auth B]	NITROSOMETHANE C H₃ N O IMHRONYAKYWGCC-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.280 (Depositor), 0.280 (DCC)
R-Value Work: 0.224 (Depositor), 0.223 (DCC)
R-Value Observed: 0.227 (Depositor)

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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-07-16

Deposition Author(s):

Revision History (Full details and data files)

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