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- PDB-3ua5: Crystal Structure of P450 2B6 (Y226H/K262R) in complex with two m... -

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Basic information

Entry
Database: PDB / ID: 3ua5
TitleCrystal Structure of P450 2B6 (Y226H/K262R) in complex with two molecules of Amlodipine
ComponentsCytochrome P450 2B6
KeywordsOXIDOREDUCTASE / P450 / human cytochrome P450 2B6 / monooxygenase / membrane protein / CYP 2B6
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 / ketone metabolic process / CYP2E1 reactions / arachidonate 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 / ketone metabolic process / CYP2E1 reactions / arachidonate 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 / 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 ...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
Amlodipine / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 2B6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsShah, M.B. / Stout, C.D. / Halpert, J.R.
CitationJournal: Biochemistry / Year: 2012
Title: Conformational Adaptation of Human Cytochrome P450 2B6 and Rabbit Cytochrome P450 2B4 Revealed upon Binding Multiple Amlodipine Molecules.
Authors: Shah, M.B. / Wilderman, P.R. / Pascual, J. / Zhang, Q. / Stout, C.D. / Halpert, J.R.
History
DepositionOct 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome P450 2B6
B: Cytochrome P450 2B6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,1608
Polymers109,2922
Non-polymers2,8686
Water1,40578
1
A: Cytochrome P450 2B6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0804
Polymers54,6461
Non-polymers1,4343
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P450 2B6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0804
Polymers54,6461
Non-polymers1,4343
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Cytochrome P450 2B6
hetero molecules

B: Cytochrome P450 2B6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,1608
Polymers109,2922
Non-polymers2,8686
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x+1/2,-y+1/2,-z1
Buried area3280 Å2
ΔGint-55 kcal/mol
Surface area38620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.000, 78.300, 247.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A28 - 492
2111B28 - 492

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Components

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


Mass: 54646.004 Da / Num. of mol.: 2 / Mutation: 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.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-06X / Amlodipine / O3-ethyl O5-methyl 2-(2-azanylethoxymethyl)-4-(2-chlorophenyl)-6-methyl-1,4-dihydropyridine-3,5-dicarboxylate


Mass: 408.876 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H25ClN2O5 / Comment: medication, channel blocker*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE 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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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M sodium acetate trihydrate, 0.1M TRIS Hcl pH 8.5 and 30% w/v PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 23, 2011
RadiationMonochromator: Si(111), side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.8→247.34 Å / Num. all: 28739 / Num. obs: 25912 / % possible obs: 90.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.131 / Rsym value: 0.131 / Net I/σ(I): 4.7
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.603 / Mean I/σ(I) obs: 1.3 / Num. unique all: 11293 / Rsym value: 0.603 / % possible all: 3.2

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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: 3IBD

3ibd


Resolution: 2.8→82.45 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.87 / SU B: 21.595 / SU ML: 0.42 / Cross valid method: THROUGHOUT / ESU R Free: 0.482 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29414 1305 5 %RANDOM
Rwork0.24214 ---
all0.24481 27295 --
obs0.24481 24667 90.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.498 Å2
Baniso -1Baniso -2Baniso -3
1-6.88 Å2-0 Å2-0 Å2
2---3.28 Å20 Å2
3----3.6 Å2
Refinement stepCycle: LAST / Resolution: 2.8→82.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7379 0 198 78 7655
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0227775
X-RAY DIFFRACTIONr_angle_refined_deg1.432.01610563
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6015924
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.05322.934351
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.398151246
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3441556
X-RAY DIFFRACTIONr_chiral_restr0.1540.21125
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215992
X-RAY DIFFRACTIONr_mcbond_it0.5161.54630
X-RAY DIFFRACTIONr_mcangle_it1.00727483
X-RAY DIFFRACTIONr_scbond_it1.32633145
X-RAY DIFFRACTIONr_scangle_it2.3664.53080
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3611 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
TIGHT POSITIONAL0.060.05
TIGHT THERMAL0.080.5
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 92 -
Rwork0.317 1627 -
obs--82.53 %

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