Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 57.18 kDa 
• Atom Count: 4069 
• Residue Count: 480 
• Unique protein chains: 1

2HI4

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

• DOI: 10.2210/pdb2HI4/pdb

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


• Deposited: 2006-06-29 Released: 2007-02-20 
• Deposition Author(s): Sansen, S., Yano, J.K., Reynald, R.L., Schoch, G.S., Stout, C.D., Johnson, E.F.

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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 

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

• PubMed: 17311915 
• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Cytochrome P450 1A2	A	495	Homo sapiens	Mutation(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 GTEx  ENSG00000140505

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	A	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
BHF	A	2-PHENYL-4H-BENZO[H]CHROMEN-4-ONE C19 H12 O2 VFMMPHCGEFXGIP-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
BHF	IC50:  234   nM  BindingDB
BHF	IC50:  49   nM  BindingDB
BHF	IC50:  30000   nM  BindingDB
BHF	IC50:  30   nM  BindingDB
BHF	IC50:  3.799999952316284   nM  BindingDB
BHF	IC50:  19   nM  BindingDB
BHF	IC50:  12   nM  BindingDB
BHF	Ki:  20   nM  BindingDB
BHF	IC50:  30   nM  BindingDB
BHF	IC50:  6   nM  BindingDB
BHF	IC50:  6   nM  BindingDB
BHF	IC50:  340   nM  BindingDB
BHF	IC50:  32600   nM  BindingDB
BHF	Ki:  25   nM  Binding MOAD
BHF	IC50:  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 = 79.63	α = 90
b = 80.82	β = 90
c = 175.82	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-06-29 
• Released Date: 2007-02-20 
Deposition Author(s): Sansen, S., Yano, J.K., Reynald, R.L., Schoch, G.S., Stout, C.D., Johnson, E.F.

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