6CSB

V308E mutant of cytochrome P450 2D6 complexed with thioridazine

PDB DOI: https://doi.org/10.2210/pdb6CSB/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free:
0.229 (Depositor), 0.230 (DCC)
R-Value Work:
0.193 (Depositor), 0.190 (DCC)
R-Value Observed:
0.195 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 222.35 kDa
Atom Count: 15,058
Modelled Residue Count: 1,814
Deposited Residue Count: 1,916
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450 2D6	A, B, C, D	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P10635
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain E [auth A] SDF format, chain L [auth B] SDF format, chain T [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain T [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain E [auth A] mmCIF format, chain L [auth B] mmCIF format, chain T [auth C]	AA [auth D], E [auth A], L [auth B], T [auth C]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain AA [auth D] Focus chain E [auth A] Focus chain L [auth B] Focus chain T [auth C] Interactions & Density Focus chain AA [auth D] Focus chain E [auth A] Focus chain L [auth B] Focus chain T [auth C]
2CV Query on 2CV Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain P [auth B] SDF format, chain X [auth C] MOL2 format, chain H [auth A] MOL2 format, chain P [auth B] MOL2 format, chain X [auth C] mmCIF format, chain H [auth A] mmCIF format, chain P [auth B] mmCIF format, chain X [auth C]	H [auth A], P [auth B], X [auth C]	HEGA-10 C₁₈ H₃₇ N O₇ ITEIKACYSCODFV-ATLSCFEFSA-N		Interactions Focus chain H [auth A] Focus chain P [auth B] Focus chain X [auth C] Interactions & Density Focus chain H [auth A] Focus chain P [auth B] Focus chain X [auth C]
RTZ Query on RTZ Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain U [auth C] SDF format, chain V [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C]	BA [auth D] CA [auth D] F [auth A] G [auth A] M [auth B] BA [auth D], CA [auth D], F [auth A], G [auth A], M [auth B], N [auth B], U [auth C], V [auth C]	10-{2-[(2R)-1-methylpiperidin-2-yl]ethyl}-2-(methylsulfanyl)-10H-phenothiazine C₂₁ H₂₆ N₂ S₂ KLBQZWRITKRQQV-MRXNPFEDSA-N		Interactions Focus chain BA [auth D] Focus chain CA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain U [auth C] Focus chain V [auth C] Interactions & Density Focus chain BA [auth D] Focus chain CA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain U [auth C] Focus chain V [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain W [auth C] MOL2 format, chain W [auth C] mmCIF format, chain W [auth C]	W [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain W [auth C] Interactions & Density Focus chain W [auth C]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] mmCIF format, chain DA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C]	DA [auth D] I [auth A] J [auth A] K [auth A] Q [auth B] DA [auth D], I [auth A], J [auth A], K [auth A], Q [auth B], R [auth B], S [auth B], Y [auth C], Z [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain DA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain DA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain Y [auth C] Focus chain Z [auth C]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain O [auth B] MOL2 format, chain O [auth B] mmCIF format, chain O [auth B]	O [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain O [auth B] Interactions & Density Focus chain O [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free: 0.229 (Depositor), 0.230 (DCC)
R-Value Work: 0.193 (Depositor), 0.190 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.738	α = 90
b = 191.999	β = 90
c = 250.46	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2019-03-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2019-03-27
Type: Initial release
Version 1.1: 2019-11-06
Changes: Author supporting evidence, Data collection
Version 1.2: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description