Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Dihedral - D2  (3D View)
Pseudo Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 32.82 kDa 
• Atom Count: 2613 
• Residue Count: 287 
• Unique protein chains: 2

1IWH

Crystal Structure of Horse Carbonmonoxyhemoglobin-Bezafibrate Complex at 1.55A Resolution: A Novel Allosteric Binding Site in R-State Hemoglobin

• DOI: 10.2210/pdb1IWH/pdb

• Classification: OXYGEN STORAGE/TRANSPORT
• Organism(s): Equus caballus
• Mutation(s): No 


• Deposited: 2002-05-15 Released: 2002-10-02 
• Deposition Author(s): Shibayama, N., Miura, S., Tame, J.R.H., Yonetani, T., Park, S.-Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.233 
• R-Value Observed: 0.175 

Literature

Crystal Structure of Horse Carbonmonoxyhemoglobin-Bezafibrate Complex at 1.55A Resolution. A Novel Allosteric Binding Site in R-State Hemoglobin

Shibayama, N., Miura, S., Tame, J.R.H., Yonetani, T., Park, S.-Y.

(2002) J Biol Chem 277: 38791-38796

• PubMed: 12122004 
• DOI: 10.1074/jbc.M205461200
• Primary Citation of Related Structures:  
  1IWH


• PubMed Abstract: 
  

Bezafibrate, an antilipidemic drug, is known as a potent allosteric effector of hemoglobin. The previously proposed mechanism for the allosteric potency of this drug was that it stabilizes and constrains the T-state of hemoglobin by specifically binding to the large central cavity of the T-state. Here we report a new allosteric binding site of fully liganded R-state hemoglobin for this drug. The high resolution crystal structure of horse carbonmonoxyhemoglobin in complex with bezafibrate reveals that the bezafibrate molecule lies near the surface of the E-helix of each alpha subunit and the complex maintains the quaternary structure of the R-state. Binding is caused by the close fit of bezafibrate into the binding pocket, which is composed of some hydrophobic residues and the heme edge, suggesting the importance of hydrophobic interactions. Upon binding of bezafibrate, the distance between Fe and the N epsilon(2) of distal His E7(alpha 58) is shortened by 0.22 A in the alpha subunit, whereas no significant structural changes are transmitted to the beta subunit. Oxygen equilibrium studies of R-state-locked hemoglobin with bezafibrate in a wet porous sol-gel indicate that bezafibrate selectively lowers the oxygen affinity of one type of subunit within the R-state, consistent with the structural data. These results disclose a new allosteric mechanism of bezafibrate and offer the first demonstration of how the allosteric effector interacts with R-state hemoglobin.

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Organizational Affiliation: 

Department of Physiology, Division of Biophysics, Jichi Medical School, Yakushiji 3311-1, Minamikawachi, Kawachi, Tochigi 329-0498, Japan. [e-mail]

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin beta chain	B	146	Equus caballus	Mutation(s): 0  Gene Names: HBB
Find proteins for P02062 (Equus caballus) Explore P02062  Go to UniProtKB:  P02062

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin alpha chain	A	141	Equus caballus	Mutation(s): 0  Gene Names: HBA
Find proteins for P01958 (Equus caballus) Explore P01958  Go to UniProtKB:  P01958

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	A, B	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
PEM	A	2-[P-[2-P-CHLOROBENZAMIDO)ETHYL]PHENOXY]-2-METHYLPROPIONIC ACID C19 H20 Cl N O4 IIBYAHWJQTYFKB-UHFFFAOYSA-N
CMO	A, B	CARBON MONOXIDE C O UGFAIRIUMAVXCW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.233 
• R-Value Observed: 0.175 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.396	α = 90
b = 107.496	β = 90
c = 86.745	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
SHELXL-97	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-05-15 
• Released Date: 2002-10-02 
Deposition Author(s): Shibayama, N., Miura, S., Tame, J.R.H., Yonetani, T., Park, S.-Y.

Revision History 

• Version 1.0: 2002-10-02
  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: 2011-11-16
  Changes: Atomic model