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- PDB-7sv2: Human Cytochrome P450 (CYP) 3A5 ternary complex with azamulin -

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Basic information

Entry
Database: PDB / ID: 7sv2
TitleHuman Cytochrome P450 (CYP) 3A5 ternary complex with azamulin
ComponentsCytochrome P450 3A5
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Inhibitor / complex / binding properties / OXIDOREDUCTASE / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
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 / Xenobiotics / oxidative demethylation / 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 / Xenobiotics / oxidative demethylation / estrogen metabolic process / retinoic acid metabolic process / retinol metabolic process / unspecific monooxygenase / aromatase activity / 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 / Chem-MWY / Cytochrome P450 3A5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsHsu, M. / Johnson, E.F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM031001 United States
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Structural characterization of the homotropic cooperative binding of azamulin to human cytochrome P450 3A5.
Authors: Hsu, M.H. / Johnson, E.F.
History
DepositionNov 18, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
C: Cytochrome P450 3A5
D: Cytochrome P450 3A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,74516
Polymers219,4504
Non-polymers6,29512
Water2,306128
1
A: Cytochrome P450 3A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4364
Polymers54,8631
Non-polymers1,5743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P450 3A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4364
Polymers54,8631
Non-polymers1,5743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cytochrome P450 3A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4364
Polymers54,8631
Non-polymers1,5743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cytochrome P450 3A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4364
Polymers54,8631
Non-polymers1,5743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.786, 134.300, 275.274
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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


Mass: 54862.586 Da / Num. of mol.: 4 / Fragment: UNP 24-497
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYP3A5 / Plasmid: PCWORI / Production host: Escherichia coli (E. coli) / Strain (production host): DH-5A / References: UniProt: P20815, unspecific monooxygenase
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MWY / (3aS,4R,5S,6R,8R,9R,9aR,10R)-6-ethyl-5-hydroxy-4,6,9,10-tetramethyl-1-oxodecahydro-3a,9-propanocyclopenta[8]annulen-8-yl [(5-amino-1H-1,2,4-triazol-3-yl)sulfanyl]acetate / Azamulin


Mass: 478.648 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C24H38N4O4S / Comment: antibiotic, inhibitor*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.21 Å3/Da / Density % sol: 44.26 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop
Details: Na Malonate, pH 6.5, 30% PEG 3350, n-decyl-beta-D-maltoside

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.3→39.56 Å / Num. obs: 85964 / % possible obs: 99.6 % / Redundancy: 12.1 % / Biso Wilson estimate: 50.98 Å2 / CC1/2: 0.996 / Net I/σ(I): 7.8
Reflection shell
Resolution (Å)Num. unique obsCC1/2Diffraction-ID
2.46-2.5142410.5991
2.3-2.3442910.2021

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Processing

Software
NameVersionClassification
JBluIce-EPICS1.19.2_4158data collection
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6mjm

6mjm


Resolution: 2.46→39.44 Å / SU ML: 0.2865 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.8963
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2233 3400 4.81 %
Rwork0.1877 67252 -
obs0.1894 70652 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.54 Å2
Refinement stepCycle: LAST / Resolution: 2.46→39.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14651 0 436 128 15215
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002815490
X-RAY DIFFRACTIONf_angle_d0.620521087
X-RAY DIFFRACTIONf_chiral_restr0.04382362
X-RAY DIFFRACTIONf_plane_restr0.0042670
X-RAY DIFFRACTIONf_dihedral_angle_d12.2226012
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.46-2.50.30741470.25122804X-RAY DIFFRACTION99.97
2.5-2.530.32141310.25012752X-RAY DIFFRACTION100
2.53-2.570.31981360.25552829X-RAY DIFFRACTION100
2.57-2.610.30741360.24442718X-RAY DIFFRACTION99.89
2.61-2.660.32791390.23652796X-RAY DIFFRACTION99.93
2.66-2.710.29511430.23742752X-RAY DIFFRACTION100
2.71-2.760.29421410.23392814X-RAY DIFFRACTION100
2.76-2.820.26351200.21812775X-RAY DIFFRACTION100
2.82-2.880.28991370.22492762X-RAY DIFFRACTION99.93
2.88-2.940.2591290.23692844X-RAY DIFFRACTION99.9
2.94-3.020.28421320.22682751X-RAY DIFFRACTION100
3.02-3.10.26861550.21622778X-RAY DIFFRACTION99.97
3.1-3.190.26691440.20042778X-RAY DIFFRACTION99.97
3.19-3.290.21471410.20072815X-RAY DIFFRACTION100
3.29-3.410.26211650.21382772X-RAY DIFFRACTION99.93
3.41-3.550.25561580.20312784X-RAY DIFFRACTION99.9
3.55-3.710.21741550.19072782X-RAY DIFFRACTION99.97
3.71-3.90.18881390.16882789X-RAY DIFFRACTION99.83
3.9-4.150.20851470.16812796X-RAY DIFFRACTION99.76
4.15-4.470.19811400.16212839X-RAY DIFFRACTION99.87
4.47-4.920.17451370.15882805X-RAY DIFFRACTION99.73
4.92-5.630.20771600.17022848X-RAY DIFFRACTION99.97
5.63-7.080.20351410.18112872X-RAY DIFFRACTION99.9
7.08-39.440.16511270.15352997X-RAY DIFFRACTION99.81
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.341840995340.3250809892930.372850446941.06005176359-0.1475574433061.26933562689-0.04554668190850.04915512774170.0435093355607-0.01374824896350.05476786984260.04881122798570.0191598379988-0.0414184655748-1.41785444417E-50.331241367251-0.05572239635830.01181825405650.262551894811-0.01261888703760.278868854398-11.95115351835.812200451740.2431705528
21.40968431157-0.322504961083-0.3808442197550.6897092048570.169360698370.946868676391-0.00387895854044-0.1930602179510.07456147287370.247077365293-0.0318624213845-0.187043106379-0.04909932021720.189600376152-0.003388006335470.420231537326-0.0905572585628-0.1853853824780.3694475927760.03806015176250.3418055203527.71648631867.470700405158.747547303
32.50329301845-0.5949501745870.1721635280171.3586417621-0.1413116099121.08782921703-0.0535457379064-0.02069078711670.1849336201730.0715561561480.03536866622790.0791893924266-0.122680764231-0.1089415102754.60391527489E-50.3189216574310.014493039969-0.02797031332820.2717120355890.009084774804820.24436714653138.578825348511.548042473722.7839466938
40.730560781282-0.1629482554380.2785259350370.9649129255020.1508920912291.19518243143-0.02295905888150.103542047309-0.0263401054367-0.1036742819280.0375993732859-0.3415076952510.1344635908580.201616316126.98213360332E-50.3037407290540.008501220955380.03263411520810.3551221477570.06519080912120.46191798530534.588354977650.524054605716.4973302083
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 23 through 495)AA23 - 4951 - 465
22(chain 'B' and resid 23 through 496)BE23 - 4961 - 465
33(chain 'C' and resid 29 through 496)CI29 - 4961 - 456
44(chain 'D' and resid 27 through 495)DM27 - 4951 - 438

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