3PM0

Structural Characterization of the Complex between Alpha-Naphthoflavone and Human Cytochrome P450 1B1 (CYP1B1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.235 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Characterization of the Complex between {alpha}-Naphthoflavone and Human Cytochrome P450 1B1.

Wang, A.Savas, U.Stout, C.D.Johnson, E.F.

(2011) J.Biol.Chem. 286: 5736-5743

  • DOI: 10.1074/jbc.M110.204420

  • PubMed Abstract: 
  • The atomic structure of human P450 1B1 was determined by x-ray crystallography to 2.7 Å resolution with α-naphthoflavone (ANF) bound in the active site cavity. Although the amino acid sequences of human P450s 1B1 and 1A2 have diverged significantly, ...

    The atomic structure of human P450 1B1 was determined by x-ray crystallography to 2.7 Å resolution with α-naphthoflavone (ANF) bound in the active site cavity. Although the amino acid sequences of human P450s 1B1 and 1A2 have diverged significantly, both enzymes exhibit narrow active site cavities, which underlie similarities in their substrate profiles. Helix I residues adopt a relatively flat conformation in both enzymes, and a characteristic distortion of helix F places Phe(231) in 1B1 and Phe(226) in 1A2 in similar positions for π-π stacking with ANF. ANF binds in a distinctly different orientation in P450 1B1 from that observed for 1A2. This reflects, in part, divergent conformations of the helix B'-C loop that are stabilized by different hydrogen-bonding interactions in the two enzymes. Additionally, differences between the two enzymes for other amino acids that line the edges of the cavity contribute to distinct orientations of ANF in the two active sites. Thus, the narrow cavity is conserved in both P450 subfamily 1A and P450 subfamily 1B with sequence divergence around the edges of the cavity that modify substrate and inhibitor binding. The conservation of these P450 1B1 active site amino acid residues across vertebrate species suggests that these structural features are conserved.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome P450 1B1
A
507Homo sapiensMutation(s): 0 
Gene Names: CYP1B1
EC: 1.14.14.1
Find proteins for Q16678 (Homo sapiens)
Go to Gene View: CYP1B1
Go to UniProtKB:  Q16678
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BHF
Query on BHF

Download SDF File 
Download CCD File 
A
2-PHENYL-4H-BENZO[H]CHROMEN-4-ONE
7,8-BENZOFLAVONE; ALPHA-NAPHTHOFLAVONE
C19 H12 O2
VFMMPHCGEFXGIP-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BHFKi: 16 nM (98) BINDINGDB
BHFIC50: 1.3 - 300 nM (98) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.235 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 84.170α = 90.00
b = 103.980β = 90.00
c = 62.970γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHASERphasing
MOSFLMdata reduction
CNSrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-12-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance