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- PDB-1w0g: Crystal structure of human cytochrome P450 3A4 -

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Basic information

Entry
Database: PDB / ID: 1w0g
TitleCrystal structure of human cytochrome P450 3A4
ComponentsCYTOCHROME P450 3A4CYP3A4
KeywordsOXIDOREDUCTASE / NIFEDIPINE OXIDASE / CYTOCHROME P450 / ELECTRON TRANSPORT / MONOOXYGENASE
Function / homology
Function and homology information


quinine 3-monooxygenase / 1,8-cineole 2-exo-monooxygenase / albendazole monooxygenase (sulfoxide-forming) / quinine 3-monooxygenase activity / 1,8-cineole 2-exo-monooxygenase activity / 1-alpha,25-dihydroxyvitamin D3 23-hydroxylase activity / vitamin D3 25-hydroxylase activity / testosterone 6-beta-hydroxylase activity / vitamin D 24-hydroxylase activity / vitamin D catabolic process ...quinine 3-monooxygenase / 1,8-cineole 2-exo-monooxygenase / albendazole monooxygenase (sulfoxide-forming) / quinine 3-monooxygenase activity / 1,8-cineole 2-exo-monooxygenase activity / 1-alpha,25-dihydroxyvitamin D3 23-hydroxylase activity / vitamin D3 25-hydroxylase activity / testosterone 6-beta-hydroxylase activity / vitamin D 24-hydroxylase activity / vitamin D catabolic process / retinoic acid 4-hydroxylase activity / aflatoxin metabolic process / caffeine oxidase activity / estrogen 16-alpha-hydroxylase activity / estrogen 2-hydroxylase activity / lipid hydroxylation / anandamide 8,9 epoxidase activity / anandamide 11,12 epoxidase activity / anandamide 14,15 epoxidase activity / alkaloid catabolic process / : / Aflatoxin activation and detoxification / Biosynthesis of maresin-like SPMs / monoterpenoid metabolic process / vitamin D metabolic process / Atorvastatin ADME / steroid catabolic process / Xenobiotics / oxidative demethylation / steroid hydroxylase activity / Phase I - Functionalization of compounds / long-chain fatty acid biosynthetic process / estrogen metabolic process / retinoic acid metabolic process / retinol metabolic process / Prednisone ADME / unspecific monooxygenase / aromatase activity / Aspirin ADME / steroid metabolic process / androgen metabolic process / xenobiotic catabolic process / steroid binding / xenobiotic metabolic process / cholesterol metabolic process / monooxygenase activity / lipid metabolic process / oxygen binding / oxidoreductase activity / iron ion binding / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane / enzyme binding / cytoplasm
Similarity search - Function
Cytochrome P450, E-class, group II / Cytochrome P450, E-class, CYP3A / 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
PROTOPORPHYRIN IX CONTAINING FE / METYRAPONE / Cytochrome P450 3A4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.73 Å
AuthorsWilliams, P.A. / Cosme, J. / Vinkovic, D.M. / Ward, A. / Angove, H.C. / Day, P.J. / Vonrhein, C. / Tickle, I.J. / Jhoti, H.
CitationJournal: Science / Year: 2004
Title: Crystal Structures of Human Cytochrome P450 3A4 Bound to Metyrapone and Progesterone
Authors: Williams, P.A. / Cosme, J. / Vinkovic, D.M. / Ward, A. / Angove, H.C. / Day, P.J. / Vonrhein, C. / Tickle, I.J. / Jhoti, H.
History
DepositionJun 3, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYTOCHROME P450 3A4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3243
Polymers55,4811
Non-polymers8432
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)77.940, 100.910, 131.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-2009-

HOH

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Components

#1: Protein CYTOCHROME P450 3A4 / CYP3A4 / QUININE 3-MONOOXYGENASE / CYPIIIA4 / NIFEDIPINE OXIDASE / NF-25 / P450-PCN1


Mass: 55481.480 Da / Num. of mol.: 1 / Fragment: SOLUBLE DOMAIN, RESIDUES 24-502
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Organ: LIVER / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): XL1 BLUE
References: UniProt: P08684, EC: 1.14.13.67, unspecific monooxygenase
#2: Chemical ChemComp-MYT / METYRAPONE / Metyrapone


Mass: 226.274 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H14N2O / Comment: medication, inhibitor*YM
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN TERMINUS TRUNCATED. THE CONFLICT SHOWN BELOW HAS HAS BEEN DESRCRIBED BY GONZALEZ ET AL., DNA VOL: ...N TERMINUS TRUNCATED. THE CONFLICT SHOWN BELOW HAS HAS BEEN DESRCRIBED BY GONZALEZ ET AL., DNA VOL: 7, PAGES 79-86, 1998.

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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: 2.4 Å3/Da / Density % sol: 47.6 %
Crystal growpH: 7.5
Details: 0.1M HEPES PH 7.5, 0.025M NACL, 7.5% (V/V) ISOPROPANOL, 10

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54
DetectorType: RIGAKU RAXIS 4 / Detector: IMAGE PLATE / Date: Nov 26, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.74→40 Å / Num. obs: 13241 / % possible obs: 94.7 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 10.8
Reflection shellResolution: 2.74→2.89 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.308 / Mean I/σ(I) obs: 2.5 / % possible all: 97.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0003Arefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W0E

1w0e


Resolution: 2.73→81.65 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.916 / SU B: 21.287 / SU ML: 0.418 / Cross valid method: THROUGHOUT / ESU R Free: 0.493 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.318 689 5.2 %RANDOM
Rwork0.234 ---
obs0.238 12577 93.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 78.73 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20 Å20 Å2
2--0.63 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 2.73→81.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3652 0 60 29 3741
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223810
X-RAY DIFFRACTIONr_bond_other_d0.0020.023545
X-RAY DIFFRACTIONr_angle_refined_deg1.7532.0085170
X-RAY DIFFRACTIONr_angle_other_deg1.0538264
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.325452
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.69123.758157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.27315676
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7191521
X-RAY DIFFRACTIONr_chiral_restr0.1230.2567
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024095
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02757
X-RAY DIFFRACTIONr_nbd_refined0.270.21231
X-RAY DIFFRACTIONr_nbd_other0.2050.24344
X-RAY DIFFRACTIONr_nbtor_refined0.2040.21895
X-RAY DIFFRACTIONr_nbtor_other0.0920.22249
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.251
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1230.24
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1810.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1710.221
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_it3.39252892
X-RAY DIFFRACTIONr_mcbond_other0.9135903
X-RAY DIFFRACTIONr_mcangle_it4.28263727
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.31561788
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.3827.51441
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
LS refinement shellResolution: 2.73→2.81 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 62 -
Rwork0.327 939 -
obs--96.71 %

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