6NQ5 | pdb_00006nq5

human (alpha met/beta hemichrome) hemoglobin with S-nitrosation at beta-Cys93

• PDB DOI: https://doi.org/10.2210/pdb6NQ5/pdb

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


• Deposited: 2019-01-19 Released: 2020-01-22 
• Deposition Author(s): Yi, J.
• Funding Organization(s): National Science Foundation (NSF, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.282 (Depositor), 0.286 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.232 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Starting Model: experimental

Literature

human (alpha met/beta hemichrome) hemoglobin with S-nitrosation at beta-Cys93

Yi, J.

To be published.

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)

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 32.36 kDa 
• Atom Count: 2,440 
• Modeled Residue Count: 285 
• 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A], D [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
FE	E [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SNC	B	L-PEPTIDE LINKING	C3 H6 N2 O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.282 (Depositor), 0.286 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.232 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.287	α = 90
b = 53.287	β = 90
c = 193.464	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-01-22 
Deposition Author(s): Yi, J.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	21271104
National Science Foundation (NSF, China)	China	21671103

Revision History  

• Version 1.0: 2020-01-22
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-10-30
  Changes: Structure summary