1Z10

Crystal Structure of Human Microsomal P450 2A6 with Coumarin Bound

• PDB DOI: https://doi.org/10.2210/pdb1Z10/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2005-03-02 Released: 2005-08-16 
• Deposition Author(s): Yano, J.K., Hsu, M.H., Griffin, K.J., Stout, C.D., Johnson, E.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.230 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 

Starting Model: experimental

Literature

Structures of human microsomal cytochrome P450 2A6 complexed with coumarin and methoxsalen

Yano, J.K., Hsu, M.H., Griffin, K.J., Stout, C.D., Johnson, E.F.

(2005) Nat Struct Mol Biol 12: 822-823

• PubMed: 16086027 
• DOI: https://doi.org/10.1038/nsmb971
• Primary Citation of Related Structures:  
  1Z10, 1Z11


• PubMed Abstract: 
  

  Human microsomal cytochrome P450 2A6 (CYP2A6) contributes extensively to nicotine detoxication but also activates tobacco-specific procarcinogens to mutagenic products. The CYP2A6 structure shows a compact, hydrophobic active site with one hydrogen bond donor, Asn297, that orients coumarin for regioselective oxidation. The inhibitor methoxsalen effectively fills the active site cavity without substantially perturbing the structure. The structure should aid the design of inhibitors to reduce smoking and tobacco-related cancers.

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Organizational Affiliation: 

Department of Molecular and Experimental Medicine, Scripps Research Institute, La Jolla, California 92037, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 221.83 kDa 
• Atom Count: 16,075 
• Modelled Residue Count: 1,858 
• Deposited Residue Count: 1,904 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cytochrome P450, family 2, subfamily A, polypeptide 6	A, B, C, D	476	Homo sapiens	Mutation(s): 0  Gene Names: CYP2A6 EC: 1.14.14.1 (PDB Primary Data), 1.14.14 (UniProt) Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P11509 (Homo sapiens) Explore P11509  Go to UniProtKB:  P11509
PHAROS:  P11509 GTEx:  ENSG00000255974

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	E [auth A], G [auth B], J [auth C], L [auth D]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
COU	F [auth A], H [auth B], K [auth C], M [auth D]	COUMARIN C9 H6 O2 ZYGHJZDHTFUPRJ-UHFFFAOYSA-N
GOL	I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.230 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.615	α = 90
b = 157.591	β = 92.25
c = 103.541	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-08-16 
Deposition Author(s): Yano, J.K., Hsu, M.H., Griffin, K.J., Stout, C.D., Johnson, E.F.

Revision History  

• Version 1.0: 2005-08-16
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description