6CSD

V308E mutant of cytochrome P450 2D6 complexed with prinomastat

• PDB DOI: https://doi.org/10.2210/pdb6CSD/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2018-03-20 Released: 2019-03-27 
• Deposition Author(s): Yang, Y.T., Fujita, K., Wang, P.F., Im, S.C., Pearl, N.M., Meagher, J., Stuckey, J., Waskell, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 
  0.236 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

Literature

Characteristic conformational changes on the distal and proximal surfaces of cytochrome P450 2D6 in response to substrate binding

Yang, Y.T., Fujita, F., Wang, P.F., Im, S.C., Pearl, N.M., Meagher, J., Stuckey, J., Waskell, L.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 111.22 kDa 
• Atom Count: 7,727 
• Modelled Residue Count: 916 
• Deposited Residue Count: 958 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A], I [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
CPS	E [auth A], K [auth B]	3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE C32 H58 N2 O7 S UMCMPZBLKLEWAF-BCTGSCMUSA-N
PN0	D [auth A], J [auth B]	Prinomastat C18 H21 N3 O5 S2 YKPYIPVDTNNYCN-INIZCTEOSA-N
ZN	F [auth A], G [auth A], H [auth A], L [auth B], M [auth B], N [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free:  0.236 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.472	α = 90
b = 126.527	β = 90
c = 192.258	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-03-27 
Deposition Author(s): Yang, Y.T., Fujita, K., Wang, P.F., Im, S.C., Pearl, N.M., Meagher, J., Stuckey, J., Waskell, L.

Revision History  

• Version 1.0: 2019-03-27
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description