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.

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), 0.220 (DCC)
R-Value Observed:
0.227 (Depositor)

Starting Model: experimental
View more details

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 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.

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
Modelled Residue Count: 286
Deposited Residue Count: 287
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P69905
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P68871
Sequence Annotations Expand
Reference Sequence LOADING

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 C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B]	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 D [auth A] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B]	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), 0.220 (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

View Full Validation Report

Ligand Structure Quality Assessment

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