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- PDB-8pqn: NQO1 bound to RBS-10 -

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Basic information

Entry
Database: PDB / ID: 8pqn
TitleNQO1 bound to RBS-10
ComponentsNAD(P)H dehydrogenase [quinone] 1
KeywordsOXIDOREDUCTASE / NQO1 / RBS-10 / quinone reductase / degrader resistance / prodrug
Function / homology
Function and homology information


response to L-glutamine / response to flavonoid / ubiquinone metabolic process / vitamin E metabolic process / vitamin K metabolic process / NADPH dehydrogenase (quinone) activity / NAD(P)H dehydrogenase (quinone) / cellular response to metal ion / NADH oxidation / cytochrome-b5 reductase activity, acting on NAD(P)H ...response to L-glutamine / response to flavonoid / ubiquinone metabolic process / vitamin E metabolic process / vitamin K metabolic process / NADPH dehydrogenase (quinone) activity / NAD(P)H dehydrogenase (quinone) / cellular response to metal ion / NADH oxidation / cytochrome-b5 reductase activity, acting on NAD(P)H / NADPH oxidation / response to tetrachloromethane / NADH:ubiquinone reductase (non-electrogenic) activity / NAD(P)H dehydrogenase (quinone) activity / response to hydrogen sulfide / response to alkaloid / response to carbohydrate / synaptic transmission, cholinergic / Regulation of ornithine decarboxylase (ODC) / NFE2L2 regulating anti-oxidant/detoxification enzymes / response to testosterone / response to amine / superoxide dismutase activity / response to electrical stimulus / nitric oxide biosynthetic process / xenobiotic metabolic process / removal of superoxide radicals / response to nutrient / response to hormone / cell redox homeostasis / response to ischemia / protein catabolic process / negative regulation of protein catabolic process / response to toxic substance / cellular response to hydrogen peroxide / protein polyubiquitination / positive regulation of neuron apoptotic process / response to estradiol / cellular response to oxidative stress / response to ethanol / response to oxidative stress / response to lipopolysaccharide / innate immune response / neuronal cell body / synapse / dendrite / negative regulation of apoptotic process / RNA binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Flavodoxin-like fold / Flavodoxin-like fold / Flavoprotein-like superfamily
Similarity search - Domain/homology
Chem-978 / FLAVIN-ADENINE DINUCLEOTIDE / NAD(P)H dehydrogenase [quinone] 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsPous, J. / Jose-Duran, F. / Mayor-Ruiz, C. / Riera, A.
Funding supportEuropean Union, Spain, 2items
OrganizationGrant numberCountry
European Research Council (ERC)101040046European Union
Spanish Ministry of Science, Innovation, and UniversitiesPID2020-120110RA-I00 Spain
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2024
Title: Discovery and Mechanistic Elucidation of NQO1-Bioactivatable Small Molecules That Overcome Resistance to Degraders.
Authors: Barbosa, B.M.G. / Sfyaki, A. / Rafael, S. / Jose-Duran, F. / Pous, J. / Sanchez-Zarzalejo, C. / Perez-Lopez, C. / Vilanova, M. / Cigler, M. / Gay, M. / Vilaseca, M. / Winter, G.E. / Riera, A. / Mayor-Ruiz, C.
History
DepositionJul 11, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.year ..._citation.journal_volume / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD(P)H dehydrogenase [quinone] 1
B: NAD(P)H dehydrogenase [quinone] 1
C: NAD(P)H dehydrogenase [quinone] 1
D: NAD(P)H dehydrogenase [quinone] 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,4078
Polymers123,1064
Non-polymers2,3024
Water00
1
A: NAD(P)H dehydrogenase [quinone] 1
B: NAD(P)H dehydrogenase [quinone] 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7044
Polymers61,5532
Non-polymers1,1512
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7720 Å2
ΔGint-48 kcal/mol
Surface area20390 Å2
2
C: NAD(P)H dehydrogenase [quinone] 1
D: NAD(P)H dehydrogenase [quinone] 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7044
Polymers61,5532
Non-polymers1,1512
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7400 Å2
ΔGint-48 kcal/mol
Surface area20810 Å2
Unit cell
Length a, b, c (Å)70.748, 178.369, 210.479
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A
32A
42A
53A
63A
74A
84A
95A
105A
116A
126A

NCS domain segments:

Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: LYS / End label comp-ID: LYS / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 1 - 273 / Label seq-ID: 1 - 273

Dom-IDComponent-IDEns-ID
111
211
322
422
533
633
744
844
955
1055
1166
1266

NCS ensembles :
IDDetails
1Global NCS restraints between domains: 1 2
2Global NCS restraints between domains: 3 4
3Global NCS restraints between domains: 5 6
4Global NCS restraints between domains: 7 8
5Global NCS restraints between domains: 9 10
6Global NCS restraints between domains: 11 12

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Components

#1: Protein
NAD(P)H dehydrogenase [quinone] 1 / Azoreductase / DT-diaphorase / DTD / Menadione reductase / NAD(P)H:quinone oxidoreductase 1 / ...Azoreductase / DT-diaphorase / DTD / Menadione reductase / NAD(P)H:quinone oxidoreductase 1 / Phylloquinone reductase / Quinone reductase 1 / QR1


Mass: 30776.412 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NQO1, DIA4, NMOR1 / Production host: Escherichia coli (E. coli)
References: UniProt: P15559, NAD(P)H dehydrogenase (quinone)
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-978 / ~{N}-[4-[(3-methylphenyl)carbonylamino]phenyl]-5-nitro-furan-2-carboxamide


Mass: 365.340 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H15N3O5 / Feature type: SUBJECT OF INVESTIGATION
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: 2.77 Å3/Da / Density % sol: 55.5 % / Description: small yellow rods.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.2 / Details: 300mM TRIS 9.2 2.8M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 25, 2023 / Details: Kirkpatrick-Baez
RadiationMonochromator: Si(111) channel-cut, cryocooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.8→89.18 Å / Num. obs: 13579 / % possible obs: 100 % / Redundancy: 6.1 % / Biso Wilson estimate: 121.5 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 11.4
Reflection shellResolution: 3.8→4.01 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 1956 / % possible all: 100

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Processing

Software
NameVersionClassification
MxCuBEdata collection
iMOSFLM7.4.0data reduction
pointless1.12.14data scaling
SCALA3.3.22data scaling
PHASER2.8.3phasing
REFMAC5.8.0405refinement
Coot0.987model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.8→68.132 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.901 / SU B: 107.197 / SU ML: 1.248 / Cross valid method: FREE R-VALUE / ESU R Free: 1.161
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3616 687 5.073 %
Rwork0.261 12856 -
all0.266 --
obs-13543 99.904 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 209.703 Å2
Baniso -1Baniso -2Baniso -3
1-31.519 Å20 Å2-0 Å2
2---11.45 Å20 Å2
3----20.069 Å2
Refinement stepCycle: LAST / Resolution: 3.8→68.132 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8696 0 160 0 8856
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0129102
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168368
X-RAY DIFFRACTIONr_angle_refined_deg0.8941.64912320
X-RAY DIFFRACTIONr_angle_other_deg0.3131.57219496
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.551088
X-RAY DIFFRACTIONr_dihedral_angle_2_deg2.302536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.012101554
X-RAY DIFFRACTIONr_dihedral_angle_6_deg11.01110396
X-RAY DIFFRACTIONr_chiral_restr0.0410.21292
X-RAY DIFFRACTIONr_chiral_restr_other0.010.22
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0210150
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021882
X-RAY DIFFRACTIONr_nbd_refined0.180.22087
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.28474
X-RAY DIFFRACTIONr_nbtor_refined0.1790.24430
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.24573
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2134
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1440.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2560.239
X-RAY DIFFRACTIONr_nbd_other0.2270.2133
X-RAY DIFFRACTIONr_mcbond_it10.39121.4754364
X-RAY DIFFRACTIONr_mcbond_other10.3921.4744364
X-RAY DIFFRACTIONr_mcangle_it17.18132.1495448
X-RAY DIFFRACTIONr_mcangle_other17.1832.1515449
X-RAY DIFFRACTIONr_scbond_it8.07421.6424738
X-RAY DIFFRACTIONr_scbond_other8.06321.6384735
X-RAY DIFFRACTIONr_scangle_it14.05632.3976872
X-RAY DIFFRACTIONr_scangle_other14.05532.3976873
X-RAY DIFFRACTIONr_lrange_it24.007291.5210609
X-RAY DIFFRACTIONr_lrange_other24.006291.52110610
Refine LS restraints NCS

Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION / Type: tight positional; tight thermal / Weight Biso : 0.866 / Weight position: 0.0866

Ens-IDDom-IDRms dev Biso (Å2)Rms dev position (Å)
1111.303340.02374
1211.303340.02374
2316.807770.02847
2416.807770.02847
3521.693650.02731
3621.693650.02731
4715.228490.02641
4815.228490.02641
5919.74980.02652
51019.74980.02652
61116.560460.02339
61216.560460.02339
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
3.8-3.8980.581660.4769110.4839780.570.63999.89780.44
3.898-4.0050.461510.4439090.4449660.7090.70799.37890.413
4.005-4.1210.463490.4328840.4349330.7270.7551000.404
4.121-4.2470.471440.4188510.428950.7920.8081000.39
4.247-4.3860.494420.3838530.3888950.7870.8351000.369
4.386-4.5390.438370.3667920.378290.8450.8621000.349
4.539-4.7090.376470.3077820.3118290.8790.9191000.299
4.709-4.9010.319450.2627410.2667870.9040.93899.87290.255
4.901-5.1170.365440.2867290.2917730.8330.9211000.275
5.117-5.3660.446340.2727040.287380.8680.9311000.265
5.366-5.6540.353320.2556530.2596850.9020.9461000.241
5.654-5.9940.298350.2146510.2186860.9360.961000.21
5.994-6.4050.388240.2365920.2436160.8740.9581000.232
6.405-6.9130.365270.225520.2275790.9130.9671000.223
6.913-7.5650.418280.1955040.2075320.9060.9711000.201
7.565-8.4450.275250.1654710.1714970.9610.98199.79880.176
8.445-9.7260.265210.1474300.1524510.9630.9861000.159
9.726-11.8520.236150.1253700.1293860.9720.99199.74090.147
11.852-16.5130.209150.1632870.1653020.970.9861000.195
16.513-68.1320.34960.3481900.3481960.8550.9211000.353

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