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- PDB-3qoa: Crystal structure of a human cytochrome P450 2B6 (Y226H/K262R) in... -

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Basic information

Entry
Database: PDB / ID: 3qoa
TitleCrystal structure of a human cytochrome P450 2B6 (Y226H/K262R) in complex with the inhibitor 4-Benzylpyridine.
ComponentsCytochrome P450 2B6
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / P450 / CYTOCHROME P450 2B6 / MONOOXYGENASE / MEMBRANE PROTEIN / CYP2B6 / ENDOPLASMIC RETICULUM / HEME / IRON / MEMBRANE / METAL BINDING / MIRCOSOME / PHOSPHOPROTEIN / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
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 / CYP2E1 reactions / arachidonic acid epoxygenase activity / 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 / CYP2E1 reactions / arachidonic acid epoxygenase activity / 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 / monooxygenase activity / xenobiotic metabolic process / 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
4-benzylpyridine / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 2B6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsShah, M.B. / Pascual, J. / Stout, C.D. / Halpert, J.R.
CitationJournal: Mol.Pharmacol. / Year: 2011
Title: Structures of Cytochrome P450 2B6 Bound to 4-Benzylpyridine and 4-(4-Nitrobenzyl)pyridine: Insight into Inhibitor Binding and Rearrangement of Active Site Side Chains.
Authors: Shah, M.B. / Pascual, J. / Zhang, Q. / Stout, C.D. / Halpert, J.R.
History
DepositionFeb 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2011Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999THE RESIDUES 3-21 (LSVLLFLALLTGLLLLLVQ) OF CORRESPONDING DATABASE REFERENCE SEQUENCE (UNP P20813) ...THE RESIDUES 3-21 (LSVLLFLALLTGLLLLLVQ) OF CORRESPONDING DATABASE REFERENCE SEQUENCE (UNP P20813) IS DELETED IN THIS STRUCTURE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome P450 2B6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4215
Polymers54,6461
Non-polymers1,7754
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.760, 76.760, 201.341
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Cytochrome P450 2B6 / CYPIIB6 / Cytochrome P450 IIB1


Mass: 54646.004 Da / Num. of mol.: 1 / Fragment: Cytochrome P450 2B6, residues 3-21 deleted
Mutation: E2A, R22K, H23K, P24T, N25S, T26S, H27K, D28G, R29K, Y226H, K262R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYP2B6 / Plasmid: pKK / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P20813, unspecific monooxygenase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: 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.: 2 / Source method: obtained synthetically / Formula: C23H42O11 / Comment: detergent*YM
#4: Chemical ChemComp-3QO / 4-benzylpyridine


Mass: 169.222 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H11N
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 3.13 Å3/Da / Density % sol: 60.75 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Ammonium acetate, 0.1 M HEPES, 25% PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 11, 2010
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.1→50.34 Å / Num. obs: 37630 / % possible obs: 91.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 23.442 Å2 / Rmerge(I) obs: 0.124 / Rsym value: 0.124 / Net I/σ(I): 4.3
Reflection shellResolution: 2.1→2.154 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 1.7 / Rsym value: 0.413 / % possible all: 92.4

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Processing

Software
NameVersionClassification
Blu-Icedata collection
BALBESphasing
REFMAC5.5.0102refinement
iMOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ME6

3me6


Resolution: 2.1→50.34 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.922 / SU B: 4.522 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24992 1885 5 %RANDOM
Rwork0.1972 ---
all0.19987 41152 --
obs0.19987 35495 90.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.442 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å20.43 Å2-0 Å2
2--0.85 Å2-0 Å2
3----1.28 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3711 0 74 250 4035
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0223888
X-RAY DIFFRACTIONr_angle_refined_deg1.872.0075269
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4395458
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.95922.747182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.37215642
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3191531
X-RAY DIFFRACTIONr_chiral_restr0.1240.2560
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212980
X-RAY DIFFRACTIONr_mcbond_it1.0861.52299
X-RAY DIFFRACTIONr_mcangle_it1.91523722
X-RAY DIFFRACTIONr_scbond_it3.15831589
X-RAY DIFFRACTIONr_scangle_it4.8924.51547
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 140 -
Rwork0.247 2592 -
obs-2592 91.74 %

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