1DT6 | pdb_00001dt6

STRUCTURE OF MAMMALIAN CYTOCHROME P450 2C5

• PDB DOI: https://doi.org/10.2210/pdb1DT6/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Oryctolagus cuniculus
• Expression System: Escherichia coli
• Mutation(s): Yes 
• Membrane Protein: Yes  OPM


• Deposited: 2000-01-11 Released: 2000-09-27 
• Deposition Author(s): Williams, P.A., Cosme, J., Sridhar, V., Johnson, E.F., McRee, D.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.313 (Depositor), 0.305 (DCC) 
• R-Value Work: 
  0.238 (Depositor), 0.234 (DCC) 
• R-Value Observed: 
  0.241 (Depositor) 

Literature

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: 121-131

• PubMed: 10678174 
• DOI: https://doi.org/10.1016/s1097-2765(00)80408-6
• Primary Citation Related Structures: 
  1DT6


• PubMed Abstract: 
  

  Microsomal cytochrome P450s participate in xenobiotic detoxification, procarcinogen activation, and steroid hormone synthesis. The first structure of a mammalian microsomal P450 suggests that the association of P450s with the endoplasmic reticulum involves a hydrophobic surface of the protein formed by noncontiguous portions of the polypeptide chain. This interaction places the entrance of the putative substrate access channel in or near the membrane and orients the face of the protein proximal to the heme cofactor perpendicular to the plane of the membrane for interaction with the P450 reductase. This structure offers a template for modeling other mammalian P450s and should aid drug discovery and the prediction of drug-drug interactions.

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Organizational Affiliation: 
• Department of Molecular Biology MB-8, Scripps Research Institute, La Jolla, California 92037, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PQS (software)

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 54.94 kDa 
• Atom Count: 3,648 
• Modeled Residue Count: 449 
• Deposited Residue Count: 473 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOCHROME P450 2C5	A	473	Oryctolagus cuniculus	Mutation(s): 11  EC: 1.14.14.1 Membrane Entity: Yes
UniProt
Find proteins for P00179 (Oryctolagus cuniculus) Explore P00179  Go to UniProtKB:  P00179

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	F [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
SM	B [auth A]	SAMARIUM (III) ION Sm DOSGOCSVHPUUIA-UHFFFAOYSA-N
SO4	C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.313 (Depositor), 0.305 (DCC) 
• R-Value Work:  0.238 (Depositor), 0.234 (DCC) 
• R-Value Observed: 0.241 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.7	α = 90
b = 132	β = 90
c = 172.4	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
SCALA	data scaling
XTALVIEW	refinement
DENZO	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-09-27 
Deposition Author(s): Williams, P.A., Cosme, J., Sridhar, V., Johnson, E.F., McRee, D.E.

Revision History  

• Version 1.0: 2000-09-27
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2018-01-31
  Changes: Experimental preparation
• Version 1.4: 2019-07-24
  Changes: Data collection, Refinement description
• Version 1.5: 2021-11-03
  Changes: Database references, Derived calculations
• Version 1.6: 2024-10-30
  Changes: Data collection, Structure summary