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- PDB-9ms2: Crystal structure of human CYP3A5 in complex with SJYHJ-111 -

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Basic information

Entry
Database: PDB / ID: 9ms2
TitleCrystal structure of human CYP3A5 in complex with SJYHJ-111
ComponentsCytochrome P450 3A5
KeywordsOXIDOREDUCTASE/INHIBITOR / Cytochrome P450 3A5 / CYP3A5 / CYP3A5-selective inhibitor / drug metabolizing enzyme / OXIDOREDUCTASE / OXIDOREDUCTASE-INHIBITOR complex
Function / homology
Function and homology information


retinoic acid 4-hydroxylase activity / aflatoxin metabolic process / lipid hydroxylation / testosterone 6-beta-hydroxylase activity / alkaloid catabolic process / Aflatoxin activation and detoxification / estrogen 16-alpha-hydroxylase activity / estrogen 2-hydroxylase activity / oxidative demethylation / Xenobiotics ...retinoic acid 4-hydroxylase activity / aflatoxin metabolic process / lipid hydroxylation / testosterone 6-beta-hydroxylase activity / alkaloid catabolic process / Aflatoxin activation and detoxification / estrogen 16-alpha-hydroxylase activity / estrogen 2-hydroxylase activity / oxidative demethylation / Xenobiotics / retinoic acid metabolic process / retinol metabolic process / estrogen metabolic process / unspecific monooxygenase / steroid metabolic process / xenobiotic catabolic process / xenobiotic metabolic process / monooxygenase activity / 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, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
: / PROTOPORPHYRIN IX CONTAINING FE / DI(HYDROXYETHYL)ETHER / Cytochrome P450 3A5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsJingheng, W. / Nithianantham, S. / Miller, D.J. / Chen, T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM118041 United States
CitationJournal: Nat Commun / Year: 2025
Title: Decoding the selective chemical modulation of CYP3A4.
Authors: Wang, J. / Nithianantham, S. / Chai, S.C. / Jung, Y.H. / Yang, L. / Ong, H.W. / Li, Y. / Zhang, Y. / Miller, D.J. / Chen, T.
History
DepositionJan 9, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450 3A5
B: Cytochrome P450 3A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,94919
Polymers109,7252
Non-polymers3,22417
Water5,891327
1
A: Cytochrome P450 3A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4169
Polymers54,8631
Non-polymers1,5548
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P450 3A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,53310
Polymers54,8631
Non-polymers1,6709
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.085, 210.688, 153.993
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-777-

HOH

21B-816-

HOH

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 54862.586 Da / Num. of mol.: 2 / Fragment: UNP 24-497
Source method: isolated from a genetically manipulated source
Details: Cytochrome P450 3A5; EC: 1.14.14.1 First residues (M) - Initiating methionine Second residue (A) - Expression Tag 5th residue from last (G) - missing residue Last 4 residues (HHHH) - Expression Tag
Source: (gene. exp.) Homo sapiens (human) / Gene: CYP3A5 / Plasmid: pCWori / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: P20815, unspecific monooxygenase

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Non-polymers , 6 types, 344 molecules

#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-A1BNX / N'-(2-chlorophenyl)-N-[(3-hydroxyphenyl)methyl]-N-[(2P)-2-(1H-imidazol-1-yl)-5-(trifluoromethyl)phenyl]urea


Mass: 486.874 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H18ClF3N4O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.41 Å3/Da / Density % sol: 48.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Li2SO4 and 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 6, 2024
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.25→34.47 Å / Num. obs: 50634 / % possible obs: 99.9 % / Redundancy: 6 % / Biso Wilson estimate: 33.2 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.066 / Rrim(I) all: 0.162 / Χ2: 1 / Net I/av σ(I): 10.1 / Net I/σ(I): 10.1
Reflection shellResolution: 2.25→2.32 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.996 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4596 / CC1/2: 0.507 / Rpim(I) all: 0.485 / Rrim(I) all: 1.186 / Χ2: 1.01

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487)refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→31.95 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2396 2623 5.18 %Random
Rwork0.1976 ---
obs0.1997 50593 99.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→31.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7175 0 219 327 7721
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047576
X-RAY DIFFRACTIONf_angle_d0.70810313
X-RAY DIFFRACTIONf_dihedral_angle_d15.5812729
X-RAY DIFFRACTIONf_chiral_restr0.0441151
X-RAY DIFFRACTIONf_plane_restr0.0071300
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.290.34261510.28992470X-RAY DIFFRACTION100
2.29-2.330.32921270.27582508X-RAY DIFFRACTION100
2.34-2.380.29591410.25522455X-RAY DIFFRACTION100
2.38-2.430.29991610.24642506X-RAY DIFFRACTION100
2.43-2.490.29621480.24442473X-RAY DIFFRACTION100
2.49-2.550.29111390.23452496X-RAY DIFFRACTION100
2.55-2.620.2671570.22962485X-RAY DIFFRACTION100
2.62-2.70.23611320.21742537X-RAY DIFFRACTION100
2.7-2.790.26091330.21942492X-RAY DIFFRACTION100
2.79-2.890.28271320.21792530X-RAY DIFFRACTION100
2.89-30.26021370.21112498X-RAY DIFFRACTION100
3-3.140.23651190.21762553X-RAY DIFFRACTION100
3.14-3.30.26611360.20332519X-RAY DIFFRACTION100
3.3-3.510.27131350.20542537X-RAY DIFFRACTION100
3.51-3.780.21891300.18722542X-RAY DIFFRACTION100
3.78-4.160.19421410.16532519X-RAY DIFFRACTION100
4.16-4.760.2011410.15942564X-RAY DIFFRACTION100
4.76-5.990.20441310.1782604X-RAY DIFFRACTION100
5.99-31.950.1941320.16332682X-RAY DIFFRACTION99

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