2D5Z

Crystal structure of T-state human hemoglobin complexed with three L35 molecules


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 

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Literature

R-state haemoglobin with low oxygen affinity: crystal structures of deoxy human and carbonmonoxy horse haemoglobin bound to the effector molecule L35

Yokoyama, T.Neya, S.Tsuneshige, A.Yonetani, T.Park, S.Y.Tame, J.R.

(2006) J Mol Biol 356: 790-801

  • DOI: 10.1016/j.jmb.2005.12.018
  • Primary Citation of Related Structures:  
    2D5X, 2D5Z, 2D60

  • PubMed Abstract: 
  • Although detailed crystal structures of haemoglobin (Hb) provide a clear understanding of the basic allosteric mechanism of the protein, and how this in turn controls oxygen affinity, recent experiments with artificial effector molecules have shown a far greater control of oxygen binding than with natural heterotropic effectors ...

    Although detailed crystal structures of haemoglobin (Hb) provide a clear understanding of the basic allosteric mechanism of the protein, and how this in turn controls oxygen affinity, recent experiments with artificial effector molecules have shown a far greater control of oxygen binding than with natural heterotropic effectors. Contrary to the established text-book view, these non-physiological compounds are able to reduce oxygen affinity very strongly without switching the protein to the T (tense) state. In an earlier paper we showed that bezafibrate (BZF) binds to a surface pocket on the alpha subunits of R state Hb, strongly reducing the oxygen affinity of this protein conformation. Here we report the crystallisation of Hb with L35, a related compound, and show that this binds to the central cavity of both R and T state Hb. The mechanism by which L35 reduces oxygen affinity is discussed, in relation to spectroscopic studies of effector binding.


    Organizational Affiliation

    Protein Design Laboratory, Graduate School of Integrated Science, Yokohama City University, 1-7-29 Suehiro, Tsurumi, Yokohama, 230-0045, Japan.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hemoglobin alpha subunitA, C141Homo sapiensMutation(s): 0 
Gene Names: HBA1HBA2
UniProt & NIH Common Fund Data Resources
Find proteins for P69905 (Homo sapiens)
Explore P69905 
Go to UniProtKB:  P69905
PHAROS:  P69905
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69905
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Hemoglobin beta subunitB, D146Homo sapiensMutation(s): 0 
Gene Names: HBB
UniProt & NIH Common Fund Data Resources
Find proteins for P68871 (Homo sapiens)
Explore P68871 
Go to UniProtKB:  P68871
PHAROS:  P68871
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68871
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
H [auth C],
J [auth D]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
L35
Query on L35

Download Ideal Coordinates CCD File 
F [auth A],
I [auth C],
K [auth D]
2-[4-({[(3,5-DICHLOROPHENYL)AMINO]CARBONYL}AMINO)PHENOXY]-2-METHYLPROPANOIC ACID
C17 H16 Cl2 N2 O4
OYJPTSMWFKGZJM-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.028α = 90
b = 82.697β = 90
c = 110.343γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-03-07
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance