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- PDB-5wbg: Crystal Structure of human Cytochrome P450 2B6 (Y226H/K262R) in c... -

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Basic information

Entry
Database: PDB / ID: 5wbg
TitleCrystal Structure of human Cytochrome P450 2B6 (Y226H/K262R) in complex with an analog of a drug Efavirenz
ComponentsCytochrome P450 2B6
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


testosterone 16-alpha-hydroxylase activity / testosterone 16-beta-hydroxylase activity / Fatty acids / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor / cellular ketone metabolic process / arachidonic acid epoxygenase activity / CYP2E1 reactions / epoxygenase P450 pathway / estrogen 2-hydroxylase activity / anandamide 8,9 epoxidase activity ...testosterone 16-alpha-hydroxylase activity / testosterone 16-beta-hydroxylase activity / Fatty acids / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor / cellular ketone metabolic process / arachidonic acid epoxygenase activity / CYP2E1 reactions / epoxygenase P450 pathway / estrogen 2-hydroxylase activity / anandamide 8,9 epoxidase activity / anandamide 11,12 epoxidase activity / anandamide 14,15 epoxidase activity / Xenobiotics / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / Phase I - Functionalization of compounds / steroid metabolic process / xenobiotic catabolic process / xenobiotic metabolic process / monooxygenase activity / iron ion binding / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane / cytoplasm
Similarity search - Function
Cytochrome P450, E-class, group I, CYP2B-like / Cytochrome P450, E-class, group I / Cytochrome p450 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-9ZJ / PROTOPORPHYRIN IX CONTAINING FE / 5-cyclohexylpentan-1-ol / Cytochrome P450 2B6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsShah, M.B. / Halpert, J.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ES003619 United States
CitationJournal: Int J Mol Sci / Year: 2018
Title: Crystal Structure of CYP2B6 in Complex with an Efavirenz Analog.
Authors: Shah, M.B. / Zhang, Q. / Halpert, J.R.
History
DepositionJun 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450 2B6
B: Cytochrome P450 2B6
C: Cytochrome P450 2B6
D: Cytochrome P450 2B6
E: Cytochrome P450 2B6
F: Cytochrome P450 2B6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)336,11224
Polymers327,8766
Non-polymers8,23618
Water2,792155
1
A: Cytochrome P450 2B6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7494
Polymers54,6461
Non-polymers1,1023
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytochrome P450 2B6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0734
Polymers54,6461
Non-polymers1,4273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cytochrome P450 2B6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0734
Polymers54,6461
Non-polymers1,4273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Cytochrome P450 2B6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0734
Polymers54,6461
Non-polymers1,4273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Cytochrome P450 2B6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0734
Polymers54,6461
Non-polymers1,4273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Cytochrome P450 2B6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0734
Polymers54,6461
Non-polymers1,4273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)103.293, 197.786, 119.222
Angle α, β, γ (deg.)90.00, 98.51, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYSERSERAA28 - 2779 - 258
21GLYGLYSERSERBB28 - 2779 - 258
31GLYGLYSERSERCC28 - 2779 - 258
41GLYGLYSERSERDD28 - 2779 - 258
51GLYGLYSERSEREE28 - 2779 - 258
61GLYGLYSERSERFF28 - 2779 - 258
12ALAALAARGARGAA279 - 491260 - 472
22ALAALAARGARGBB279 - 491260 - 472
32ALAALAARGARGCC279 - 491260 - 472
42ALAALAARGARGDD279 - 491260 - 472
52ALAALAARGARGEE279 - 491260 - 472
62ALAALAARGARGFF279 - 491260 - 472

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Cytochrome P450 2B6 / 1 / 4-cineole 2-exo-monooxygenase / CYPIIB6 / Cytochrome P450 IIB1


Mass: 54646.004 Da / Num. of mol.: 6 / Fragment: residues 30-491 / Mutation: Y226H, K262R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYP2B6 / Plasmid: pKKdH
Details (production host): N-terminally truncated and engineered construct with His-tag at the C-terminus
Production host: Escherichia coli (E. coli) / Strain (production host): JM109
References: UniProt: P20813, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor

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Non-polymers , 5 types, 173 molecules

#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-9ZJ / (2R,4S)-6-chloro-4-(cyclopropylethynyl)-2-methyl-4-(trifluoromethyl)-1,4-dihydro-2H-3,1-benzoxazine


Mass: 315.718 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C15H13ClF3NO
#4: Chemical ChemComp-ZAZ / 5-cyclohexylpentan-1-ol


Mass: 170.292 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H22O
#5: Chemical
ChemComp-CM5 / 5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE / 5-CYCLOHEXYLPENTYL 4-O-ALPHA-D-GLUCOPYRANOSYL-BETA-D-GLUCOPYRANOSIDE / CYMAL-5


Mass: 494.573 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C23H42O11 / Comment: detergent*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.77 Å3/Da / Density % sol: 67.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 0.8M Sodium Formate 0.1 M Tris pH 7.5 8% w/v PEG 20000 8% v/v PEG 550 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.1808
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 8, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1808 Å / Relative weight: 1
ReflectionResolution: 2.99→50 Å / Num. obs: 89926 / % possible obs: 98.9 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.188 / Net I/σ(I): 6.4
Reflection shellResolution: 2.99→3.07 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 1.6 / % possible all: 96.7

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4I91

4i91


Resolution: 2.99→50 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.896 / SU B: 20.491 / SU ML: 0.37 / Cross valid method: THROUGHOUT / ESU R: 0.699 / ESU R Free: 0.4 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.262 4745 5 %RANDOM
Rwork0.227 ---
obs0.229 89926 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 49.63 Å2
Baniso -1Baniso -2Baniso -3
1--2.57 Å20 Å23.2 Å2
2---2.59 Å20 Å2
3---6.1 Å2
Refinement stepCycle: LAST / Resolution: 2.99→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21849 0 566 155 22570
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02223090
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6592.01531457
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.45952770
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.23222.9871021
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.02153543
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.53615145
X-RAY DIFFRACTIONr_chiral_restr0.10.23438
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02117631
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1852tight positional0.050.05
2B1852tight positional0.060.05
3C1852tight positional0.050.05
4D1852tight positional0.050.05
5E1852tight positional0.040.05
6F1852tight positional0.040.05
1A1760medium positional0.060.5
2B1760medium positional0.070.5
3C1760medium positional0.060.5
4D1760medium positional0.060.5
5E1760medium positional0.060.5
6F1760medium positional0.050.5
LS refinement shellResolution: 2.99→3.07 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 364 -
Rwork0.331 6642 -
obs--99.73 %

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