Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 109.60 kDa 
• Atom Count: 7445 
• Residue Count: 922 
• Unique protein chains: 1

3QM4

Human Cytochrome P450 (CYP) 2D6 - Prinomastat Complex

• DOI: 10.2210/pdb3QM4/pdb

• Classification: OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli DH5[alpha]
• Mutation(s): No 


• Deposited: 2011-02-03 Released: 2012-02-15 
• Deposition Author(s): Wang, A., Stout, C.D., Johnson, E.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 0.288 
• R-Value Work: 0.243 
• R-Value Observed: 0.245 

Literature

Crystal Structure of Human Cytochrome P450 2D6 with Prinomastat Bound.

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

(2012) J Biol Chem 287: 10834-10843

• PubMed: 22308038 
• DOI: 10.1074/jbc.M111.307918
• Primary Citation of Related Structures:  
  3QM4


• PubMed Abstract: 
  

Human cytochrome P450 2D6 contributes to the metabolism of >15% of drugs used in clinical practice. This study determined the structure of P450 2D6 complexed with a substrate and potent inhibitor, prinomastat, to 2.85 Å resolution by x-ray crystallography. Prinomastat binding is well defined by electron density maps with its pyridyl nitrogen bound to the heme iron. The structure of ligand-bound P450 2D6 differs significantly from the ligand-free structure reported for the P450 2D6 Met-374 variant (Protein Data Bank code 2F9Q). Superposition of the structures reveals significant differences for β sheet 1, helices A, F, F', G", G, and H as well as the helix B-C loop. The structure of the ligand complex exhibits a closed active site cavity that conforms closely to the shape of prinomastat. The closure of the open cavity seen for the 2F9Q structure reflects a change in the direction and pitch of helix F and introduction of a turn at Gly-218, which is followed by a well defined helix F' that was not observed in the 2F9Q structure. These differences reflect considerable structural flexibility that is likely to contribute to the catalytic versatility of P450 2D6, and this new structure provides an alternative model for in silico studies of substrate interactions with P450 2D6.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450 2D6	A, B	479	Homo sapiens	Mutation(s): 0  Gene Names: CYP2D6, CYP2DL1 EC: 1.14.14.1 (PDB Primary Data), 1.14.14 (UniProt)
Find proteins for P10635 (Homo sapiens) Explore P10635  Go to UniProtKB:  P10635
NIH Common Fund Data Resources
PHAROS:  P10635 GTEx:  ENSG00000100197

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	A, B	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
PN0	A, B	Prinomastat C18 H21 N3 O5 S2 YKPYIPVDTNNYCN-INIZCTEOSA-N
NI	B	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 0.288 
• R-Value Work: 0.243 
• R-Value Observed: 0.245 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 194.54	α = 90
b = 55.07	β = 134.97
c = 145.87	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-02-03 
• Released Date: 2012-02-15 
Deposition Author(s): Wang, A., Stout, C.D., Johnson, E.F.

Revision History 

• Version 1.0: 2012-02-15
  Type: Initial release
  
• Version 1.1: 2012-02-22
  Changes: Database references
• Version 1.2: 2012-07-04
  Changes: Database references
• Version 1.3: 2012-07-18
  Changes: Database references