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- PDB-6mjm: Substrate Free Cytochrome P450 3A5 (CYP3A5) -

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Basic information

Entry
Database: PDB / ID: 6mjm
TitleSubstrate Free Cytochrome P450 3A5 (CYP3A5)
ComponentsCytochrome P450 3A5
KeywordsOXIDOREDUCTASE / cytochrome P450 / monooxygenase / membrane protein / drug metabolism
Function / homology
Function and homology information


testosterone 6-beta-hydroxylase activity / retinoic acid 4-hydroxylase activity / aflatoxin metabolic process / estrogen 16-alpha-hydroxylase activity / lipid hydroxylation / alkaloid catabolic process / Aflatoxin activation and detoxification / oxidative demethylation / Xenobiotics / estrogen metabolic process ...testosterone 6-beta-hydroxylase activity / retinoic acid 4-hydroxylase activity / aflatoxin metabolic process / estrogen 16-alpha-hydroxylase activity / lipid hydroxylation / alkaloid catabolic process / Aflatoxin activation and detoxification / oxidative demethylation / Xenobiotics / estrogen metabolic process / retinol metabolic process / retinoic acid metabolic process / unspecific monooxygenase / aromatase activity / steroid metabolic process / xenobiotic catabolic process / monooxygenase activity / xenobiotic metabolic process / oxygen binding / oxidoreductase activity / iron ion binding / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane
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 / Cytochrome P450 3A5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHsu, M.H. / Johnson, E.F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM031001 United States
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Active-site differences between substrate-free and ritonavir-bound cytochrome P450 (CYP) 3A5 reveal plasticity differences between CYP3A5 and CYP3A4.
Authors: Hsu, M.H. / Johnson, E.F.
History
DepositionSep 21, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 29, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome P450 3A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7555
Polymers54,8631
Non-polymers8934
Water88349
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-29 kcal/mol
Surface area19770 Å2
Unit cell
Length a, b, c (Å)75.670, 100.690, 136.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Cytochrome P450 3A5 / CYPIIIA5 / Cytochrome P450 HLp2 / Cytochrome P450-PCN3


Mass: 54862.586 Da / Num. of mol.: 1 / Fragment: UNP 24-497
Source method: isolated from a genetically manipulated source
Details: SEQADV 5VEU MET A 22 UNP P20815 INITIATING METHIONINE SEQADV 5VEU ALA A 23 UNP P20815 EXPRESSION TAG SEQADV 5VEU HIS A 498 UNP P20815 EXPRESSION TAG SEQADV 5VEU HIS A 499 UNP P20815 ...Details: SEQADV 5VEU MET A 22 UNP P20815 INITIATING METHIONINE SEQADV 5VEU ALA A 23 UNP P20815 EXPRESSION TAG SEQADV 5VEU HIS A 498 UNP P20815 EXPRESSION TAG SEQADV 5VEU HIS A 499 UNP P20815 EXPRESSION TAG SEQADV 5VEU HIS A 500 UNP P20815 EXPRESSION TAG SEQADV 5VEU HIS A 501 UNP P20815 EXPRESSION TAG
Source: (gene. exp.) Homo sapiens (human) / Gene: CYP3A5 / Plasmid: PCWORI / Production host: Escherichia coli (E. coli) / Strain (production host): DH5[alpha] / References: UniProt: P20815, 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.36 Å3/Da / Density % sol: 47.91 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, ADA, Anapoe 20

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.2→38.89 Å / Num. obs: 26713 / % possible obs: 99.8 % / Redundancy: 9.7 % / CC1/2: 1 / Net I/σ(I): 34.47
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 9.7 % / Mean I/σ(I) obs: 3.87 / Num. unique obs: 1940 / CC1/2: 0.924 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1tqn

1tqn


Resolution: 2.2→34.274 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / Phase error: 29.17
RfactorNum. reflection% reflection
Rfree0.248 1353 5.07 %
Rwork0.2092 --
obs0.2112 26710 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→34.274 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3630 0 61 49 3740
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053782
X-RAY DIFFRACTIONf_angle_d0.7445129
X-RAY DIFFRACTIONf_dihedral_angle_d11.9122296
X-RAY DIFFRACTIONf_chiral_restr0.045570
X-RAY DIFFRACTIONf_plane_restr0.004643
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2004-2.2790.32921240.272482X-RAY DIFFRACTION99
2.279-2.37020.32411150.24632531X-RAY DIFFRACTION100
2.3702-2.47810.30261370.25212491X-RAY DIFFRACTION100
2.4781-2.60870.28541310.24742514X-RAY DIFFRACTION100
2.6087-2.7720.30021480.25882508X-RAY DIFFRACTION100
2.772-2.9860.32211340.2652535X-RAY DIFFRACTION100
2.986-3.28620.35081370.25872522X-RAY DIFFRACTION100
3.2862-3.76120.27881410.22092536X-RAY DIFFRACTION100
3.7612-4.73680.22751360.17572572X-RAY DIFFRACTION100
4.7368-34.2740.18041500.1792666X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 18.5489 Å / Origin y: 23.7448 Å / Origin z: 15.6501 Å
111213212223313233
T0.4282 Å2-0.0411 Å2-0.1226 Å2-0.4517 Å20.0348 Å2--0.4284 Å2
L1.7754 °20.5858 °20.171 °2-3.0686 °20.287 °2--1.7375 °2
S0.0066 Å °0.0952 Å °0.2524 Å °0.3603 Å °-0.1017 Å °-0.3749 Å °-0.3035 Å °0.2141 Å °0.0836 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 26 through 496)

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