3T3S

Human Cytochrome P450 2A13 in complex with Pilocarpine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural comparison of cytochromes P450 2A6, 2A13, and 2E1 with pilocarpine.

DeVore, N.M.Meneely, K.M.Bart, A.G.Stephens, E.S.Battaile, K.P.Scott, E.E.

(2012) FEBS J 279: 1621-1631

  • DOI: 10.1111/j.1742-4658.2011.08412.x
  • Primary Citation of Related Structures:  
    3T3Q, 3T3Z, 3T3R, 3T3S

  • PubMed Abstract: 
  • Human xenobiotic-metabolizing cytochrome P450 (CYP) enzymes can each bind and monooxygenate a diverse set of substrates, including drugs, often producing a variety of metabolites. Additionally, a single ligand can interact with multiple CYP enzymes, but often the protein structural similarities and differences that mediate such overlapping selectivity are not well understood ...

    Human xenobiotic-metabolizing cytochrome P450 (CYP) enzymes can each bind and monooxygenate a diverse set of substrates, including drugs, often producing a variety of metabolites. Additionally, a single ligand can interact with multiple CYP enzymes, but often the protein structural similarities and differences that mediate such overlapping selectivity are not well understood. Even though the CYP superfamily has a highly canonical global protein fold, there are large variations in the active site size, topology, and conformational flexibility. We have determined how a related set of three human CYP enzymes bind and interact with a common inhibitor, the muscarinic receptor agonist drug pilocarpine. Pilocarpine binds and inhibits the hepatic CYP2A6 and respiratory CYP2A13 enzymes much more efficiently than the hepatic CYP2E1 enzyme. To elucidate key residues involved in pilocarpine binding, crystal structures of CYP2A6 (2.4 Å), CYP2A13 (3.0 Å), CYP2E1 (2.35 Å), and the CYP2A6 mutant enzyme, CYP2A6 I208S/I300F/G301A/S369G (2.1 Å) have been determined with pilocarpine in the active site. In all four structures, pilocarpine coordinates to the heme iron, but comparisons reveal how individual residues lining the active sites of these three distinct human enzymes interact differently with the inhibitor pilocarpine.


    Organizational Affiliation

    Department of Medicinal Chemistry, The University of Kansas, Lawrence, KS 66045, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome P450 2A13A, B, C, D, E, F, G, H476Homo sapiensMutation(s): 0 
Gene Names: CYP2A13
EC: 1.14.14.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q16696 (Homo sapiens)
Explore Q16696 
Go to UniProtKB:  Q16696
PHAROS:  Q16696
Protein Feature View
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  • Reference Sequence
Small Molecules
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
9PLKd:  3000   nM  BindingDB
9PLKi:  3000   nM  BindingDB
9PLKi:  1400   nM  BindingDB
9PLKd:  3600   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.218 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.501α = 101.01
b = 119.862β = 101.72
c = 154.871γ = 93.59
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-12-07
    Type: Initial release
  • Version 1.1: 2012-06-06
    Changes: Database references
  • Version 1.2: 2017-11-08
    Changes: Refinement description