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- PDB-6fy4: Structure of human NAD(P) H:quinone oxidoreductase in complex wit... -

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Basic information

Entry
Database: PDB / ID: 6fy4
TitleStructure of human NAD(P) H:quinone oxidoreductase in complex with N-(2-bromophenyl)pyrrolidine-1-sulfonamide
ComponentsNAD(P)H dehydrogenase [quinone] 1
KeywordsOXIDOREDUCTASE / flavoprotein ligand complex quinone reduction oxidative stress drug metabolism
Function / homology
Function and homology information


response to L-glutamine / response to flavonoid / ubiquinone metabolic process / response to hydrogen sulfide / vitamin E metabolic process / vitamin K metabolic process / NADPH dehydrogenase (quinone) activity / NAD(P)H dehydrogenase (quinone) / NADH oxidation / cellular response to metal ion ...response to L-glutamine / response to flavonoid / ubiquinone metabolic process / response to hydrogen sulfide / vitamin E metabolic process / vitamin K metabolic process / NADPH dehydrogenase (quinone) activity / NAD(P)H dehydrogenase (quinone) / NADH oxidation / cellular response to metal ion / 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 / synaptic transmission, cholinergic / response to alkaloid / response to carbohydrate / 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 hormone / response to nutrient / 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 / dendrite / neuronal cell body / synapse / negative regulation of apoptotic process / RNA binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Flavodoxin-like fold / Flavodoxin-like fold / Flavodoxin domain / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N-(2-bromophenyl)pyrrolidine-1-sulfonamide / FLAVIN-ADENINE DINUCLEOTIDE / NAD(P)H dehydrogenase [quinone] 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å
AuthorsGruber, K. / Hromic, A.
CitationJournal: Febs Lett. / Year: 2020
Title: A small molecule chaperone rescues the stability and activity of a cancer-associated variant of NAD(P)H:quinone oxidoreductase 1 in vitro.
Authors: Strandback, E. / Lienhart, W.D. / Hromic-Jahjefendic, A. / Bourgeois, B. / Hogler, A. / Waltenstorfer, D. / Winkler, A. / Zangger, K. / Madl, T. / Gruber, K. / Macheroux, P.
History
DepositionMar 10, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: 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

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)127,0789
Polymers123,6304
Non-polymers3,4475
Water0
1
A: NAD(P)H dehydrogenase [quinone] 1
B: NAD(P)H dehydrogenase [quinone] 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6925
Polymers61,8152
Non-polymers1,8763
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8380 Å2
ΔGint-51 kcal/mol
Surface area21750 Å2
MethodPISA
2
C: NAD(P)H dehydrogenase [quinone] 1
D: NAD(P)H dehydrogenase [quinone] 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3864
Polymers61,8152
Non-polymers1,5712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8100 Å2
ΔGint-52 kcal/mol
Surface area21880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.369, 121.369, 158.252
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112

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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: 30907.611 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 BL21(DE3) (bacteria) / Variant (production host): Gold pLysS AG
References: UniProt: P15559, NAD(P)H dehydrogenase (quinone)
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-EAW / N-(2-bromophenyl)pyrrolidine-1-sulfonamide


Mass: 305.191 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13BrN2O2S

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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: 2.72 Å3/Da / Density % sol: 54.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.9
Details: 0.2 M magnesium chloride hexahydrate, 20% w/v polyethylene glycol 3350, pH 5.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0009 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 1, 2017 / Details: Si-111 and Si-113 reflection
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0009 Å / Relative weight: 1
ReflectionResolution: 2.76→87.56 Å / Num. obs: 34531 / % possible obs: 100 % / Redundancy: 18.6 % / Biso Wilson estimate: 49 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.158 / Rpim(I) all: 0.038 / Rrim(I) all: 0.162 / Net I/σ(I): 15.1
Reflection shellResolution: 2.76→2.89 Å / Redundancy: 17.9 % / Rmerge(I) obs: 0.587 / Mean I/σ(I) obs: 5.3 / Num. unique obs: 4561 / CC1/2: 0.95 / Rpim(I) all: 0.142 / Rrim(I) all: 0.604 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CET

4cet


Resolution: 2.76→52.751 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2902 1717 4.98 %random selection
Rwork0.218 ---
obs0.2216 34483 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.76→52.751 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8616 0 228 0 8844
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099113
X-RAY DIFFRACTIONf_angle_d1.2112358
X-RAY DIFFRACTIONf_dihedral_angle_d9.895240
X-RAY DIFFRACTIONf_chiral_restr0.0621292
X-RAY DIFFRACTIONf_plane_restr0.0081538
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.76-2.84130.38661330.3042707X-RAY DIFFRACTION100
2.8413-2.9330.40641200.30262724X-RAY DIFFRACTION100
2.933-3.03780.36791420.29322714X-RAY DIFFRACTION100
3.0378-3.15940.35411320.28292719X-RAY DIFFRACTION100
3.1594-3.30320.36111420.27292702X-RAY DIFFRACTION100
3.3032-3.47730.32211550.24682708X-RAY DIFFRACTION100
3.4773-3.69510.28841540.22482730X-RAY DIFFRACTION100
3.6951-3.98030.28881270.20982732X-RAY DIFFRACTION100
3.9803-4.38070.25981580.19382719X-RAY DIFFRACTION100
4.3807-5.01410.271310.1732748X-RAY DIFFRACTION100
5.0141-6.31560.24571410.19692758X-RAY DIFFRACTION100
6.3156-52.76030.24821820.17852805X-RAY DIFFRACTION100

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