Biological Assembly 1  

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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: 32821.37 
• Atom Count: 2318 
• 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


• 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 

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


• 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

Find similar proteins by: Sequence  |  Structure

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

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
PEM	A	2-[P-[2-P-CHLOROBENZAMIDO)ETHYL]PHENOXY]-2-METHYLPROPIONIC ACID C19 H20 Cl N O4 IIBYAHWJQTYFKB-UHFFFAOYSA-N
HEM	A, B	PROTOPORPHYRIN IX CONTAINING FE HEME C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
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 
• Space Group: C 2 2 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 62.396	α = 90.00
b = 107.496	β = 90.00
c = 86.745	γ = 90.00

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
DENZO	data reduction
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
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2011-11-16
  Type: Atomic model