2HBS

THE HIGH RESOLUTION CRYSTAL STRUCTURE OF DEOXYHEMOGLOBIN S


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The high resolution crystal structure of deoxyhemoglobin S.

Harrington, D.J.Adachi, K.Royer Jr., W.E.

(1997) J Mol Biol 272: 398-407

  • DOI: 10.1006/jmbi.1997.1253
  • Primary Citation of Related Structures:  
    2HBS

  • PubMed Abstract: 
  • We have refined the crystal structure of deoxyhemoglobin S (beta Glu6-->Val) at 2.05 A resolution to an R-factor of 16.5% (free R=21. 5%) using crystals isomorphous to those originally grown by Wishner and Love. A predominant feature of this crystal ...

    We have refined the crystal structure of deoxyhemoglobin S (beta Glu6-->Val) at 2.05 A resolution to an R-factor of 16.5% (free R=21. 5%) using crystals isomorphous to those originally grown by Wishner and Love. A predominant feature of this crystal form is a double strand of hemoglobin tetramers that has been shown by a variety of techniques to be the fundamental building block of the intracellular sickle cell fiber. The double strand is stabilized by lateral contacts involving the mutant valine interacting with a pocket between the E and F helices on another tetramer. The new structure reveals some marked differences from the previously refined 3.0 A resolution structure, including several residues in the lateral contact which have shifted by as much as 3.5 A. The lateral contact includes, in addition to the hydrophobic interactions involving the mutant valine, hydrophilic interactions and bridging water molecules at the periphery of the contact. This structure provides further insights into hemoglobin polymerization and may be useful for the structure-based design of therapeutic agents to treat sickle cell disease.


    Related Citations: 
    • Refined Crystal Structure of Deoxyhemoglobin S. II. Molecular Interactions in the Crystal
      Padlan, E.A., Love, W.E.
      (1985) J Biol Chem 260: 8280
    • Refined Crystal Structure of Deoxyhemoglobin S. I. Restrained Least-Squares Refinement at 3.0-A Resolution
      Padlan, E.A., Love, W.E.
      (1985) J Biol Chem 260: 8272
    • Intermolecular Interactions in Crystals of Human Deoxy Hemoglobin A, C, F and S
      Love, W.E., Fitzgerald, P.M.D., Hanson, J.C., Royer Junior, W.E.
      (1978) Inserm Symp 9: 65
    • Crystal Structure of Sickle-Cell Deoxyhemoglobin
      Wishner, B.C., Hanson, J.C., Ringle, W.M., Love, W.E.
      (1976) Proceedings Of The Symposium On Molecular And Cellular Aspects Of Sickle Cell Disease, Dallas, Texas, December 10, 1975 (in: Dhew Pub (nih) (us), No 76-1007) --: 1
    • Crystals of Deoxy Sickle Cell Hemoglobin
      Wishner, B.C., Love, W.E.
      (1975) Proceedings Of The First National Symposium On Sickle Cell Disease, Washington, D C , June 27-29, 1974 (in: Dhew Pub (nih) (us), No 75-723) --: 85
    • Crystal Structure of Sickle-Cell Deoxyhemoglobin at 5 A Resolution
      Wishner, B.C., Ward, K.B., Lattman, E.E., Love, W.E.
      (1975) J Mol Biol 98: 179

    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA 01605, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HEMOGLOBIN S (DEOXY), ALPHA CHAINACEG141Homo sapiensMutation(s): 0 
Gene Names: HBA1HBA2
Find proteins for P69905 (Homo sapiens)
Explore P69905 
Go to UniProtKB:  P69905
NIH Common Fund Data Resources
PHAROS  P69905
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HEMOGLOBIN S (DEOXY), BETA CHAINBDFH146Homo sapiensMutation(s): 1 
Gene Names: HBB
Find proteins for P68871 (Homo sapiens)
Explore P68871 
Go to UniProtKB:  P68871
NIH Common Fund Data Resources
PHAROS  P68871
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.165 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.344α = 90
b = 185.681β = 92.74
c = 52.933γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-07-23
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-02-01
    Changes: Structure summary