2HI4

Crystal Structure of Human Microsomal P450 1A2 in complex with alpha-naphthoflavone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Adaptations for the oxidation of polycyclic aromatic hydrocarbons exhibited by the structure of human P450 1A2.

Sansen, S.Yano, J.K.Reynald, R.L.Schoch, G.A.Griffin, K.J.Stout, C.D.Johnson, E.F.

(2007) J Biol Chem 282: 14348-14355

  • DOI: 10.1074/jbc.M611692200
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Microsomal cytochrome P450 family 1 enzymes play prominent roles in xenobiotic detoxication and procarcinogen activation. P450 1A2 is the principal cytochrome P450 family 1 enzyme expressed in human liver and participates extensively in drug oxidatio ...

    Microsomal cytochrome P450 family 1 enzymes play prominent roles in xenobiotic detoxication and procarcinogen activation. P450 1A2 is the principal cytochrome P450 family 1 enzyme expressed in human liver and participates extensively in drug oxidations. This enzyme is also of great importance in the bioactivation of mutagens, including the N-hydroxylation of arylamines. P450-catalyzed reactions involve a wide range of substrates, and this versatility is reflected in a structural diversity evident in the active sites of available P450 structures. Here, we present the structure of human P450 1A2 in complex with the inhibitor alpha-naphthoflavone, determined to a resolution of 1.95 A. alpha-Naphthoflavone is bound in the active site above the distal surface of the heme prosthetic group. The structure reveals a compact, closed active site cavity that is highly adapted for the positioning and oxidation of relatively large, planar substrates. This unique topology is clearly distinct from known active site architectures of P450 family 2 and 3 enzymes and demonstrates how P450 family 1 enzymes have evolved to catalyze efficiently polycyclic aromatic hydrocarbon oxidation. This report provides the first structure of a microsomal P450 from family 1 and offers a template to study further structure-function relationships of alternative substrates and other cytochrome P450 family 1 members.


    Organizational Affiliation

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



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome P450 1A2A495Homo sapiensMutation(s): 0 
Gene Names: CYP1A2
EC: 1.14.14.1 (PDB Primary Data), 4.2.1.152 (UniProt)
Find proteins for P05177 (Homo sapiens)
Explore P05177 
Go to UniProtKB:  P05177
NIH Common Fund Data Resources
PHAROS  P05177
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
BHF
Query on BHF

Download CCD File 
A
2-PHENYL-4H-BENZO[H]CHROMEN-4-ONE
C19 H12 O2
VFMMPHCGEFXGIP-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BHFIC50:  234   nM  BindingDB
BHFIC50:  49   nM  BindingDB
BHFIC50:  30000   nM  BindingDB
BHFIC50:  30   nM  BindingDB
BHFIC50:  3.799999952316284   nM  BindingDB
BHFIC50:  19   nM  BindingDB
BHFIC50:  12   nM  BindingDB
BHFKi:  20   nM  BindingDB
BHFIC50:  30   nM  BindingDB
BHFIC50:  6   nM  BindingDB
BHFIC50:  6   nM  BindingDB
BHFIC50:  340   nM  BindingDB
BHFIC50:  32600   nM  BindingDB
BHFKi:  25   nM  Binding MOAD
BHFIC50:  32000   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.223 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.63α = 90
b = 80.82β = 90
c = 175.82γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
CCP4data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-02-20
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description