1N6B

Microsomal Cytochrome P450 2C5/3LVdH Complex with a dimethyl derivative of sulfaphenazole


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.257 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of a Substrate Complex of Mammalian Cytochrome P450 2C5 at 2.3 A Resolution: Evidence for Multiple Substrate Binding Modes

Wester, M.R.Johnson, E.F.Marques-Soares, C.Dansette, P.M.Mansuy, D.Stout, C.D.

(2003) Biochemistry 42: 6370-6379

  • DOI: 10.1021/bi0273922

  • PubMed Abstract: 
  • The structure of rabbit microsomal cytochrome P450 2C5/3LVdH complexed with a substrate, 4-methyl-N-methyl-N-(2-phenyl-2H-pyrazol-3-yl)benzenesulfonamide (DMZ), was determined by X-ray crystallography to 2.3 A resolution. Substrate docking studies an ...

    The structure of rabbit microsomal cytochrome P450 2C5/3LVdH complexed with a substrate, 4-methyl-N-methyl-N-(2-phenyl-2H-pyrazol-3-yl)benzenesulfonamide (DMZ), was determined by X-ray crystallography to 2.3 A resolution. Substrate docking studies and electron density maps indicate that DMZ binds to the enzyme in two antiparallel orientations of the long axis of the substrate. One orientation places the principal site of hydroxylation, the 4-methyl group, 4.4 A from the heme Fe, whereas the alternate conformation positions the second, infrequent site of hydroxylation at >5.9 A from the heme Fe. Comparison of this structure to that obtained previously for the enzyme indicates that the protein closes around the substrate and prevents open access of water from bulk solvent to the heme Fe. This reflects a approximately 1.5 A movement of the F and G helices relative to helix I. The present structure provides a complete model for the protein from residues 27-488 and defines two new helices F' and G'. The G' helix is likely to contribute to interactions of the enzyme with membranes. The relatively large active site, as compared to the volume occupied by the substrate, and the flexibility of the enzyme are likely to underlie the capacity of drug-metabolizing enzymes to metabolize structurally diverse substrates of different sizes.


    Related Citations: 
    • Mammalian Microsomal Cytochrome P450 Monooxygenase: Structural Adaptations for Membrane Binding and Functional Diversity
      Williams, P.A.,Cosme, J.,Sridhar, V.,Johnson, E.F.,McRee, D.E.
      (2000) Mol.Cell 5: 121
    • Engineering Microsomal Cytochrome P450 2C5 to be a Soluble, Monomeric Enzyme. Mutations that Alter Aggregation, Phospholipid Dependence of Catalysis, and Membrane Binding
      Cosme, J.,Johnson, E.F.
      (2000) J.Biol.Chem. 275: 2545


    Organizational Affiliation

    Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, MEM-255, La Jolla, California 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome P450 2C5
A
473Oryctolagus cuniculusMutations: R188E, I189L, S192T, undefined1M, undefined5T, undefined2A, undefined6S, undefined7S, N184H, undefined8K, undefined3K, undefined4K, S191G
Gene Names: CYP2C5
EC: 1.14.14.1
Find proteins for P00179 (Oryctolagus cuniculus)
Go to UniProtKB:  P00179
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 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
DMZ
Query on DMZ

Download SDF File 
Download CCD File 
A
4-METHYL-N-METHYL-N-(2-PHENYL-2H-PYRAZOL-3-YL)BENZENESULFONAMIDE
DIMETHYLSULFAPHENAZOLE
C17 H17 N3 O2 S
KRHPBWNETCEFGS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DMZKd: 20000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.257 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 74.330α = 90.00
b = 134.290β = 90.00
c = 171.840γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
CNSphasing
CNSrefinement
SCALAdata scaling
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-06-03
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance