Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 57224.74 
• Atom Count: 3880 
• Residue Count: 476 
• Unique protein chains: 1

4I91

Crystal Structure of Cytochrome P450 2B6 (Y226H/K262R) in complex with alpha-Pinene.

• DOI: 10.2210/pdb4I91/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): 11 


• Deposited: 2012-12-04 Released: 2013-07-03 
• Deposition Author(s): Shah, M.B., Stout, C.D., Halpert, J.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.210 
• R-Value Work: 0.181 

Literature

Structural and Thermodynamic Basis of (+)-alpha-Pinene Binding to Human Cytochrome P450 2B6.

Wilderman, P.R., Shah, M.B., Jang, H.H., Stout, C.D., Halpert, J.R.

(2013) J.Am.Chem.Soc. 135: 10433-10440

• PubMed: 23786449 
• DOI: 10.1021/ja403042k


• PubMed Abstract: 
  

Despite recent advances in atomic-level understanding of drug and inhibitor interactions with human cytochromes P450, the decades-old questions of chemical and structural determinants of hydrocarbon binding are still unanswered. (+)-α-Pinene is a monoterpene hydrocarbon that is widely distributed in the environment and a potent P450 2B inhibitor. Therefore, a combined biophysical and structural analysis of human P450 2B6 interactions with (+)-α-pinene was undertaken to elucidate the basis of the very high affinity binding. Binding of (+)-α-pinene to the P450 active site was demonstrated by a Type I spectral shift. Thermodynamics of ligand binding were explored using isothermal titration calorimetry and compared to those of P450 2A6, which is much less flexible than 2B6 based on comparison of multiple X-ray crystal structures. Consistent with expectation, entropy is the major driving force for hydrocarbon binding to P450 2A6, as evidenced by the calorimetric results. However, formation of the 2B6-(+)-α-pinene complex has a significant enthalpic component. A 2.0 Å resolution crystal structure of this enzyme-ligand complex reveals that the highly plastic 2B6 utilizes previously unrecognized rearrangements of protein motifs. The results indicate that the specific components of enthalpic contribution to ligand binding are closely tied to the degree of enzyme flexibility.

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Organizational Affiliation: 

Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Cytochrome P450 2B6	A	476	Homo sapiens	Mutation(s): 11  Gene Names: CYP2B6 EC: 1.14.13.-
Find proteins for P20813 (Homo sapiens) Go to Gene View: CYP2B6 Go to UniProtKB:  P20813

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SUC	A	SUCROSE C12 H22 O11 CZMRCDWAGMRECN-UGDNZRGBSA-N
TMH	A	(+)-alpha-Pinene (+)-3,6,6-TRIMETHYLBICYCLO[3.1.1]HEPT-2-ENE C10 H16 GRWFGVWFFZKLTI-RKDXNWHRSA-N
CM5	A	5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE 5-CYCLOHEXYLPENTYL 4-O-ALPHA-D-GLUCOPYRANOSYL-BETA-D-GLUCOPYRANOSIDE; CYMAL-5 C23 H42 O11 RVTGFZGNOSKUDA-ZNGNCRBCSA-N
HEM	A	PROTOPORPHYRIN IX CONTAINING FE HEME C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
TMH	Kd: 220 nM BINDINGMOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.210 
• R-Value Work: 0.181 
• Space Group: P 3₂ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 77.059	α = 90.00
b = 77.059	β = 90.00
c = 201.847	γ = 120.00

Software Package:

Software Name	Purpose
Blu-Ice	data collection
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-12-04 
• Released Date: 2013-07-03 
• Deposition Author(s): Shah, M.B., Stout, C.D., Halpert, J.R.

Revision History 

• Version 1.0: 2013-07-03
  Type: Initial release
• Version 1.1: 2013-08-28
  Type: Database references
• Version 1.2: 2014-12-31
  Type: Non-polymer description