3D17

A triply ligated crystal structure of relaxed state human hemoglobin

• PDB DOI: https://doi.org/10.2210/pdb3D17/pdb

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


• Deposited: 2008-05-05 Released: 2008-06-03 
• Deposition Author(s): Safo, M.K., Musayev, F.N., Jenkins, J., Abraham, D.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.297 
• R-Value Work: 0.232 
• R-Value Observed: 0.255 

Literature

A triply ligated crystal structure of relaxed state human hemoglobin

Jenkins, J., Musayev, F.N., Abraham, D.J., Safo, M.K.

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)

Macromolecule Content

• Total Structure Weight: 65.01 kDa 
• Atom Count: 4,672 
• Modelled Residue Count: 574 
• Deposited Residue Count: 574 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit alpha	A, C	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, D	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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	E [auth A], J [auth B], L [auth C], N [auth D]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
PO4	H [auth B], I [auth B], M [auth D]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
MBN	F [auth A]	TOLUENE C7 H8 YXFVVABEGXRONW-UHFFFAOYSA-N
CMO	G [auth A], K [auth B], O [auth D]	CARBON MONOXIDE C O UGFAIRIUMAVXCW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.297 
• R-Value Work: 0.232 
• R-Value Observed: 0.255 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.282	α = 90
b = 87.282	β = 90
c = 174.466	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
AMoRE	phasing
CNS	refinement
PDB_EXTRACT	data extraction
d*TREK	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-06-03 
Deposition Author(s): Safo, M.K., Musayev, F.N., Jenkins, J., Abraham, D.J.

Revision History  

• Version 1.0: 2008-06-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description