PDB-2f9q: Crystal Structure of Human Cytochrome P450 2D6

ID or keywords:

Entry

Database: PDB / ID: 2f9q

Title

Crystal Structure of Human Cytochrome P450 2D6

Components

Cytochrome P450 2D6

CYP2D6

Keywords

OXIDOREDUCTASE /

Cytochrome P450 2D6 /

Haem

Function / homology

Function and homology information

negative regulation of binding / negative regulation of cellular organofluorine metabolic process / Miscellaneous substrates / isoquinoline alkaloid metabolic process /

Fatty acids / coumarin metabolic process /

Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen into the other donor / CYP2E1 reactions / arachidonic acid metabolic process / anandamide 8,9 epoxidase activity ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.002 Å

Authors

Rowland, P.

Citation

Journal: J.Biol.Chem. / Year: 2006
Title: Crystal Structure of Human Cytochrome P450 2D6
Authors: Rowland, P. / Blaney, F.E. / Smyth, M.G. / Jones, J.J. / Leydon, V.R. / Oxbrow, A.K. / Lewis, C.J. / Tennant, M.G. / Modi, S. / Eggleston, D.S. / Chenery, R.J. / Bridges, A.M.

History

Deposition	Dec 6, 2005	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 20, 2005	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.3	Oct 20, 2021	Group: Database references / Derived calculations Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4	Feb 14, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2f9q.cif.gz	355.3 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f9/2f9q ftp://data.pdbj.org/pub/pdb/validation_reports/f9/2f9q	HTTPS FTP

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Related structure data

Similar structure data	6vjb-d 5tvg-1 5nv4-d 1vko-1 3ks7-d 1sq4-1 3rik-d 5xyr-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#82 - Oct 2006 Cytochrome p450 similarity (2) #155 - Nov 2012 Vitamin D Receptor similarity (1)

Deposited unit

A: Cytochrome P450 2D6

B: Cytochrome P450 2D6

C: Cytochrome P450 2D6

D: Cytochrome P450 2D6

hetero molecules

218 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

2

B: Cytochrome P450 2D6

C: Cytochrome P450 2D6

hetero molecules

A: Cytochrome P450 2D6

D: Cytochrome P450 2D6

hetero molecules

defined by software
218 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	145.066, 155.495, 95.801
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Ens-ID: 1 / Refine code: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	PRO	PRO	PRO	PRO	A	A	34 - 39	12 - 17
2	1	PRO	PRO	PRO	PRO	B	B	34 - 39	12 - 17
3	1	PRO	PRO	PRO	PRO	C	C	34 - 39	12 - 17
4	1	PRO	PRO	PRO	PRO	D	D	34 - 39	12 - 17
5	2	THR	THR	GLY	GLY	A	A	54 - 95	32 - 73
6	2	THR	THR	GLY	GLY	B	B	54 - 95	32 - 73
7	2	THR	THR	GLY	GLY	C	C	54 - 95	32 - 73
8	2	THR	THR	GLY	GLY	D	D	54 - 95	32 - 73
9	3	ASP	ASP	PRO	PRO	A	A	97 - 114	75 - 92
10	3	ASP	ASP	PRO	PRO	B	B	97 - 114	75 - 92
11	3	ASP	ASP	PRO	PRO	C	C	97 - 114	75 - 92
12	3	ASP	ASP	PRO	PRO	D	D	97 - 114	75 - 92
13	4	SER	SER	ARG	ARG	A	A	116 - 123	94 - 101
14	4	SER	SER	ARG	ARG	B	B	116 - 123	94 - 101
15	4	SER	SER	ARG	ARG	C	C	116 - 123	94 - 101
16	4	SER	SER	ARG	ARG	D	D	116 - 123	94 - 101
17	5	GLY	GLY	ARG	ARG	A	A	125 - 132	103 - 110
18	5	GLY	GLY	ARG	ARG	B	B	125 - 132	103 - 110
19	5	GLY	GLY	ARG	ARG	C	C	125 - 132	103 - 110
20	5	GLY	GLY	ARG	ARG	D	D	125 - 132	103 - 110
21	6	PHE	PHE	LEU	LEU	A	A	134 - 139	112 - 117
22	6	PHE	PHE	LEU	LEU	B	B	134 - 139	112 - 117
23	6	PHE	PHE	LEU	LEU	C	C	134 - 139	112 - 117
24	6	PHE	PHE	LEU	LEU	D	D	134 - 139	112 - 117
25	7	ASN	ASN	GLY	GLY	A	A	141 - 143	119 - 121
26	7	ASN	ASN	GLY	GLY	B	B	141 - 143	119 - 121
27	7	ASN	ASN	GLY	GLY	C	C	141 - 143	119 - 121
28	7	ASN	ASN	GLY	GLY	D	D	141 - 143	119 - 121
29	8	GLY	GLY	GLU	GLU	A	A	145 - 150	123 - 128
30	8	GLY	GLY	GLU	GLU	B	B	145 - 150	123 - 128
31	8	GLY	GLY	GLU	GLU	C	C	145 - 150	123 - 128
32	8	GLY	GLY	GLU	GLU	D	D	145 - 150	123 - 128
33	9	TRP	TRP	GLY	GLY	A	A	152 - 192	130 - 170
34	9	TRP	TRP	GLY	GLY	B	B	152 - 192	130 - 170
35	9	TRP	TRP	GLY	GLY	C	C	152 - 192	130 - 170
36	9	TRP	TRP	GLY	GLY	D	D	152 - 192	130 - 170
37	10	ARG	ARG	LEU	LEU	A	A	194 - 206	172 - 184
38	10	ARG	ARG	LEU	LEU	B	B	194 - 206	172 - 184
39	10	ARG	ARG	LEU	LEU	C	C	194 - 206	172 - 184
40	10	ARG	ARG	LEU	LEU	D	D	194 - 206	172 - 184
41	11	LEU	LEU	LEU	LEU	A	A	208 - 213	186 - 191
42	11	LEU	LEU	LEU	LEU	B	B	208 - 213	186 - 191
43	11	LEU	LEU	LEU	LEU	C	C	208 - 213	186 - 191
44	11	LEU	LEU	LEU	LEU	D	D	208 - 213	186 - 191
45	12	GLU	GLU	LEU	LEU	A	A	215 - 220	193 - 198
46	12	GLU	GLU	LEU	LEU	B	B	215 - 220	193 - 198
47	12	GLU	GLU	LEU	LEU	C	C	215 - 220	193 - 198
48	12	GLU	GLU	LEU	LEU	D	D	215 - 220	193 - 198
49	13	GLU	GLU	ASP	ASP	A	A	222 - 252	200 - 230
50	13	GLU	GLU	ASP	ASP	B	B	222 - 252	200 - 230
51	13	GLU	GLU	ASP	ASP	C	C	222 - 252	200 - 230
52	13	GLU	GLU	ASP	ASP	D	D	222 - 252	200 - 230
53	14	LEU	LEU	HIS	HIS	A	A	254 - 258	232 - 236
54	14	LEU	LEU	HIS	HIS	B	B	254 - 258	232 - 236
55	14	LEU	LEU	HIS	HIS	C	C	254 - 258	232 - 236
56	14	LEU	LEU	HIS	HIS	D	D	254 - 258	232 - 236
57	15	THR	THR	PRO	PRO	A	A	261 - 268	239 - 246
58	15	THR	THR	PRO	PRO	B	B	261 - 268	239 - 246
59	15	THR	THR	PRO	PRO	C	C	261 - 268	239 - 246
60	15	THR	THR	PRO	PRO	D	D	261 - 268	239 - 246
61	16	ASP	ASP	MET	MET	A	A	270 - 279	248 - 257
62	16	ASP	ASP	MET	MET	B	B	270 - 279	248 - 257
63	16	ASP	ASP	MET	MET	C	C	270 - 279	248 - 257
64	16	ASP	ASP	MET	MET	D	D	270 - 279	248 - 257
65	17	ALA	ALA	ALA	ALA	A	A	282	260
66	17	ALA	ALA	ALA	ALA	B	B	282	260
67	17	ALA	ALA	ALA	ALA	C	C	282	260
68	17	ALA	ALA	ALA	ALA	D	D	282	260
69	18	GLY	GLY	ILE	ILE	A	A	284 - 382	262 - 360
70	18	GLY	GLY	ILE	ILE	B	B	284 - 382	262 - 360
71	18	GLY	GLY	ILE	ILE	C	C	284 - 382	262 - 360
72	18	GLY	GLY	ILE	ILE	D	D	284 - 382	262 - 360
73	19	VAL	VAL	TRP	TRP	A	A	384 - 409	362 - 387
74	19	VAL	VAL	TRP	TRP	B	B	384 - 409	362 - 387
75	19	VAL	VAL	TRP	TRP	C	C	384 - 409	362 - 387
76	19	VAL	VAL	TRP	TRP	D	D	384 - 409	362 - 387
77	20	LYS	LYS	GLY	GLY	A	A	411 - 439	389 - 417
78	20	LYS	LYS	GLY	GLY	B	B	411 - 439	389 - 417
79	20	LYS	LYS	GLY	GLY	C	C	411 - 439	389 - 417
80	20	LYS	LYS	GLY	GLY	D	D	411 - 439	389 - 417
81	21	ARG	ARG	HEM	HEM	A	A - E	441 - 600	419
82	21	ARG	ARG	HEM	HEM	B	B - H	441 - 600	419
83	21	ARG	ARG	HEM	HEM	C	C - I	441 - 600	419
84	21	ARG	ARG	HEM	HEM	D	D - J	441 - 600	419

#1: Protein	Cytochrome P450 2D6 / CYP2D6 / E.C.1.14.14.1 / CYPIID6 / P450-DB1 / Debrisoquine 4-hydroxylase Mass: 53808.598 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CYP2D6 / Production host: Escherichia coli (E. coli) / References: UniProt: P10635, unspecific monooxygenase
#2: Chemical	ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃₄H₃₂FeN₄O₄
#3: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

Crystal	Density Matthews: 2.51 Å³/Da / Density % sol: 50.96 %
Crystal grow	Temperature: 293 K / Method: liquid diffusion / pH: 5.6 Details: 1.5M ammonium sulphate, 0.1M sodium citrate, 0.2M potassium sodium tartrate, pH 5.6, LIQUID DIFFUSION, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9538 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 1, 2004
Radiation	Monochromator: Unknown / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9538 Å / Relative weight: 1
Reflection	Resolution: 3→106 Å / Num. all: 94111 / Num. obs: 39448 / % possible obs: 90 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shell	Resolution: 3→3.11 Å / % possible all: 90.7

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHASER		phasing
REFMAC	5.2	refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.002→106 Å / Cor.coef. F_o:F_c: 0.919 / Cor.coef. F_o:F_c free: 0.833 / SU B: 54.322 / SU ML: 0.449 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.558 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.28607	1601	4.1 %	RANDOM
R_work	0.2297	-	-	-
all	0.23198	39438	-	-
obs	0.23198	37837	89.58 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 57.121 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.5 Å²	0 Å²	0 Å²
2-	-	0.13 Å²	0 Å²
3-	-	-	-2.63 Å²

Refinement step

Cycle: LAST / Resolution: 3.002→106 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14228	0	182	11	14421

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.022	14822
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.647	1.998	20214
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.778	5	1802
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.941	22.711	686
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	22.112	15	2312
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.994	15	140
X-RAY DIFFRACTION	r_chiral_restr	0.109	0.2	2184
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	11536
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.249	0.2	7197
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.323	0.2	10043
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.192	0.2	494
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.336	0.2	98
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.366	0.2	5
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.435	1.5	9250
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.741	2	14638
X-RAY DIFFRACTION	r_scbond_it	1.244	3	6215
X-RAY DIFFRACTION	r_scangle_it	2.11	4.5	5568
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Number: 3377 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Type	Rms dev position (Å)	Weight position
1	A	tight positional	0.06	0.05
2	B	tight positional	0.06	0.05
3	C	tight positional	0.06	0.05
4	D	tight positional	0.06	0.05
1	A	tight thermal	0.1	0.5
2	B	tight thermal	0.1	0.5
3	C	tight thermal	0.11	0.5
4	D	tight thermal	0.09	0.5

LS refinement shell

Resolution: 3.002→3.08 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.449	115	-
R_work	0.374	2604	-
obs	-	-	85.16 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	2.6519	-0.1795	-0.5256	2.0492	-0.4372	1.8928	-0.1221	-0.0169	0.14	-0.1546	-0.0415	-0.0829	0.0074	0.1688	0.1636	-0.3541	0.0286	-0.0127	-0.052	0.0983	-0.1291	-15.3597	48.7698	-5.7656
2	2.2861	0.2849	-0.7657	2.056	-0.4387	2.2829	-0.0295	0.0247	-0.1012	0.1956	-0.1182	0.1388	0.1843	-0.0362	0.1477	0.094	0.1158	0.0295	-0.2631	-0.0354	-0.189	-34.0901	29.827	-51.994
3	2.4772	-0.1517	0.6657	3.2442	0.2038	1.4801	-0.1232	-0.0117	-0.2273	-0.0608	0.0711	0.1069	-0.1018	-0.247	0.0521	-0.3175	0.0863	0.0197	-0.0941	0.0261	-0.1843	-55.265	48.6442	-4.4768
4	2.4415	0.0372	0.5861	2.5653	1.0963	1.8387	0.2976	0.1426	-0.0396	-0.6519	-0.3852	0.0296	-0.3251	-0.1762	0.0876	0.2678	0.2431	-0.039	-0.1854	0.0255	-0.2175	-39.6085	69.4234	-51.0519

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	34 - 497
2	X-RAY DIFFRACTION	2	B	34 - 497
3	X-RAY DIFFRACTION	3	C	34 - 497
4	X-RAY DIFFRACTION	4	D	34 - 497

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