1KD2 | pdb_00001kd2

Crystal Structure of Human Deoxyhemoglobin in Absence of Any Anions

• PDB DOI: https://doi.org/10.2210/pdb1KD2/pdb

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


• Deposited: 2001-11-12 Released: 2003-06-10 
• Deposition Author(s): Colombo, M.F., Seixas, F.A.V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 
  0.250 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.187 (DCC) 

Starting Model: experimental

Literature

The X-Ray Structure of Iso-Ionic Deoxy-Hb Crystal: The High Affinity T-state of Human Hb and the Mechanism of Chloride Regulation of Hb Cooperative Oxygen Binding.

Seixas, F.A.V., Azevedo Jr, W.F., Colombo, M.F.

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: 64.55 kDa 
• Atom Count: 4,717 
• Modeled Residue Count: 574 
• Deposited Residue Count: 574 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin alpha chain	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 beta chain	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	E [auth A], F [auth B], G [auth C], H [auth D]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free:  0.250 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.187 (DCC) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.339	α = 90
b = 99.348	β = 90
c = 66.123	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
X-PLOR	refinement
REFMAC	refinement
XTALVIEW	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-06-10 
Deposition Author(s): Colombo, M.F., Seixas, F.A.V.

Revision History  

• Version 1.0: 2003-06-10
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-16
  Changes: Data collection, Database references, Derived calculations, Refinement description