1B86

HUMAN DEOXYHAEMOGLOBIN-2,3-DIPHOSPHOGLYCERATE COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

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

  • DOI: 10.1006/jmbi.1993.1505

  • 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 str ...

    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.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (HEMOGLOBIN; ALPHA CHAIN)
A, C
141Homo sapiensMutation(s): 0 
Gene Names: HBA1, HBA2
Find proteins for P69905 (Homo sapiens)
Go to Gene View: HBA1 HBA2
Go to UniProtKB:  P69905
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (HEMOGLOBIN; BETA CHAIN)
B, D
146Homo sapiensMutation(s): 0 
Gene Names: HBB
Find proteins for P68871 (Homo sapiens)
Go to Gene View: HBB
Go to UniProtKB:  P68871
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OXY
Query on OXY

Download SDF File 
Download CCD File 
A, C
OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
 Ligand Interaction
DG2
Query on DG2

Download SDF File 
Download CCD File 
D
(2R)-2,3-diphosphoglyceric acid
2,3-Bisphosphoglyceric acid; 2,3-bisphosphoglycerate; 2,3-BPG; 2,3-diphosphoglyceric acid; 2,3-diphosphoglycerate; 2,3-DPG; (2~{R})-2,3-diphosphonooxypropanoic acid
C3 H8 O10 P2
XOHUEYCVLUUEJJ-UWTATZPHSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B, C, D
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Work: 0.169 
  • Space Group: P 21 21 2 A
Unit Cell:
Length (Å)Angle (°)
a = 96.300α = 90.00
b = 98.080β = 90.00
c = 65.760γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-02-14
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-09-07
    Type: Non-polymer description, Other, Refinement description