1B86

HUMAN DEOXYHAEMOGLOBIN-2,3-DIPHOSPHOGLYCERATE COMPLEX

• PDB DOI: https://doi.org/10.2210/pdb1B86/pdb

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


• Deposited: 1999-02-08 Released: 1999-02-14 
• Deposition Author(s): Richard, V., Dodson, G.G., Mauguen, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work: 0.169 
• R-Value Observed: 0.169 

Literature

Human deoxyhaemoglobin-2,3-diphosphoglycerate complex low-salt structure at 2.5 A resolution.

Richard, V., Dodson, G.G., Mauguen, Y.

(1993) J Mol Biol 233: 270-274

• PubMed: 8377203 
• DOI: https://doi.org/10.1006/jmbi.1993.1505
• Primary Citation of Related Structures:  
  1B86


• PubMed Abstract: 
  

  The haemoglobin-2,3-diphosphoglycerate complex structure has been solved at 2.5 A resolution using crystals grown from low-salt solutions. The results show some important differences with the precedent haemoglobin-2,3-diphosphoglycerate high-salt structure solved by Arnone. First, we observe a loss of symmetry in the binding site, secondly both of the lysine residues 82 beta interact with 2,3-diphosphoglycerate at the same time, each making two contacts. This level of interaction is in agreement with the functional behaviour of natural haemoglobin mutants with mutations at the 2,3-diphosphoglycerate binding site.

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Organizational Affiliation: 

Department of Chemistry, University of York Heslington, U.K.

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.

Macromolecule Content

• Total Structure Weight: 64.88 kDa 
• Atom Count: 4,715 
• Modelled Residue Count: 574 
• Deposited Residue Count: 574 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (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
PROTEIN (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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	E [auth A], G [auth B], H [auth C], J [auth D]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
DG2	K [auth D]	(2R)-2,3-diphosphoglyceric acid C3 H8 O10 P2 XOHUEYCVLUUEJJ-UWTATZPHSA-N
OXY	F [auth A], I [auth C]	OXYGEN MOLECULE O2 MYMOFIZGZYHOMD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work: 0.169 
• R-Value Observed: 0.169 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.3	α = 90
b = 98.08	β = 90
c = 65.76	γ = 90

Software Package:

Software Name	Purpose
PROLSQ	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-02-14 
Deposition Author(s): Richard, V., Dodson, G.G., Mauguen, Y.

Revision History  

• Version 1.0: 1999-02-14
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2011-09-07
  Changes: Non-polymer description, Other, Refinement description
• Version 2.0: 2023-02-08
  Type: Remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other
• Version 2.1: 2023-03-15
  Changes: Advisory
• Version 2.2: 2024-05-22
  Changes: Data collection