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- PDB-5fuq: CRYSTAL STRUCTURE OF THE H80R VARIANT OF NQO1 BOUND TO DICOUMAROL -

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Basic information

Entry
Database: PDB / ID: 5fuq
TitleCRYSTAL STRUCTURE OF THE H80R VARIANT OF NQO1 BOUND TO DICOUMAROL
ComponentsNAD(P)H DEHYDROGENASE [QUINONE] 1
KeywordsOXIDOREDUCTASE / NADPH-QUINONE OXIDOREDUCTASE 1 / NQO1 / FAD / DICOUMAROL
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) / NADH oxidation / cellular response to metal ion / 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) / 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 / 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 / cell redox homeostasis / response to hormone / 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 / 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
ACETATE ION / BISHYDROXY[2H-1-BENZOPYRAN-2-ONE,1,2-BENZOPYRONE] / FLAVIN-ADENINE DINUCLEOTIDE / NAD(P)H dehydrogenase [quinone] 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsGavira, J.A. / Medina-Carmona, E. / Pey, A.L.
CitationJournal: Hum.Mol.Genet. / Year: 2017
Title: Enhanced vulnerability of human proteins towards disease-associated inactivation through divergent evolution.
Authors: Medina-Carmona, E. / Fuchs, J.E. / Gavira, J.A. / Mesa-Torres, N. / Neira, J.L. / Salido, E. / Palomino-Morales, R. / Burgos, M. / Timson, D.J. / Pey, A.L.
History
DepositionJan 29, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / database_2 / pdbx_database_status / struct_site
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Jan 10, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,66911
Polymers61,8532
Non-polymers2,8169
Water7,134396
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11300 Å2
ΔGint-60.9 kcal/mol
Surface area20840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.828, 104.828, 201.908
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein NAD(P)H DEHYDROGENASE [QUINONE] 1 / AZOREDUCTASE / DT-DIAPHORASE / DTD / MENADIONE REDUCTASE / NADPH / QUINONE OXIDOREDUCTASE 1 / ...AZOREDUCTASE / DT-DIAPHORASE / DTD / MENADIONE REDUCTASE / NADPH / QUINONE OXIDOREDUCTASE 1 / PHYLLOQUINONE REDUCTASE / QUINONE REDUCTASE 1 / QR1 / NADPH DEHYDROGENASE QUINONE 1


Mass: 30926.658 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET46 EK/LIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
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.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-DTC / BISHYDROXY[2H-1-BENZOPYRAN-2-ONE,1,2-BENZOPYRONE] / DICOUMAROL / Dicoumarol


Mass: 336.295 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C19H12O6 / Comment: anticoagulant, inhibitor*YM
#4: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 396 / 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: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growpH: 9
Details: CAPILLARY COUNTERDIFFUSION METHOD: 30% OF PEG 3350, 200 MM SODIUM-ACETATE, 100 MM SODIUM-TRICINE AT PH 9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.977
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2015 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.04→49.83 Å / Num. obs: 72281 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 8.9 % / Biso Wilson estimate: 43.63 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.38
Reflection shellResolution: 2.04→2.11 Å / Redundancy: 8.8 % / Rmerge(I) obs: 1.49 / Mean I/σ(I) obs: 1.45 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1D4A

1d4a


Resolution: 2.04→49.828 Å / SU ML: 0.21 / σ(F): 1.34 / Phase error: 18.29 / Stereochemistry target values: ML / Details: H80R MUTANT
RfactorNum. reflection% reflection
Rfree0.1768 3646 5 %
Rwork0.1589 --
obs0.1598 72272 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.87 Å2
Refinement stepCycle: LAST / Resolution: 2.04→49.828 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4348 0 197 396 4941
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074961
X-RAY DIFFRACTIONf_angle_d0.9266753
X-RAY DIFFRACTIONf_dihedral_angle_d14.662914
X-RAY DIFFRACTIONf_chiral_restr0.066691
X-RAY DIFFRACTIONf_plane_restr0.005863
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.04-2.06690.32091250.30662603X-RAY DIFFRACTION100
2.0669-2.09520.30741420.28692593X-RAY DIFFRACTION100
2.0952-2.12510.30261380.26562603X-RAY DIFFRACTION100
2.1251-2.15680.25661360.23672581X-RAY DIFFRACTION100
2.1568-2.19050.24571450.2222612X-RAY DIFFRACTION100
2.1905-2.22640.24361400.21782597X-RAY DIFFRACTION100
2.2264-2.26480.24361380.2062574X-RAY DIFFRACTION100
2.2648-2.3060.21621490.19692609X-RAY DIFFRACTION100
2.306-2.35040.22791250.19572638X-RAY DIFFRACTION100
2.3504-2.39840.19631160.18192637X-RAY DIFFRACTION100
2.3984-2.45050.21081410.17162590X-RAY DIFFRACTION100
2.4505-2.50750.20461530.17122613X-RAY DIFFRACTION100
2.5075-2.57020.19341450.15922593X-RAY DIFFRACTION100
2.5702-2.63970.18071360.17772637X-RAY DIFFRACTION100
2.6397-2.71740.21061230.17142626X-RAY DIFFRACTION100
2.7174-2.80510.21081470.1682622X-RAY DIFFRACTION100
2.8051-2.90530.20091480.17132624X-RAY DIFFRACTION100
2.9053-3.02160.19451480.17032633X-RAY DIFFRACTION100
3.0216-3.15910.18831310.17712662X-RAY DIFFRACTION100
3.1591-3.32560.18931540.16682617X-RAY DIFFRACTION100
3.3256-3.5340.19581490.15432656X-RAY DIFFRACTION100
3.534-3.80670.1661530.14312649X-RAY DIFFRACTION100
3.8067-4.18960.12811470.13282696X-RAY DIFFRACTION100
4.1896-4.79550.12631380.11142708X-RAY DIFFRACTION100
4.7955-6.04010.15191330.13592746X-RAY DIFFRACTION100
6.0401-49.84270.14591460.15612907X-RAY DIFFRACTION100
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)
13.65445.4712-0.18038.5538-0.52656.5532-0.30460.36480.6862-0.42970.38560.5652-0.6306-0.1178-0.16440.3079-0.0103-0.05070.4069-0.02350.5038-16.902834.1022-43.6863
23.05142.512-0.40112.8101-1.74082.8137-0.07350.15940.1642-0.3236-0.11430.4531-0.1753-0.24520.07770.34530.0137-0.05470.4705-0.05150.4514-22.570437.1416-42.5739
32.7416-2.6595-0.79843.07530.43991.2179-0.02760.04770.2617-0.49510.0628-0.0221-0.1161-0.046-0.03650.3726-0.0844-0.03780.4094-0.06590.4246-9.706329.3073-45.7382
48.4004-4.93070.01168.7751-4.8033.9241-0.03320.3599-0.321-0.2758-0.3743-0.77980.34970.65790.33350.4345-0.00780.06590.6168-0.11750.525113.970921.0461-44.7275
51.84250.101-0.0870.7938-0.07671.068-0.0626-0.20960.3423-0.02890.08310.0062-0.16710.0987-0.02170.3223-0.0434-0.02220.4141-0.10920.4084-5.051731.6762-33.7852
64.62772.5094-1.10384.8841-1.16392.4721-0.0929-0.18150.4727-0.29980.08040.3416-0.2071-0.30590.04260.29040.0656-0.01380.4804-0.11680.4558-26.48236.1728-33.1751
73.1193-1.29631.06281.5817-0.08031.9405-0.1379-0.39430.513-0.00290.131-0.3749-0.11880.15720.05280.3974-0.0306-0.02130.5423-0.21120.5793.156539.7659-19.7999
85.32651.93334.58494.93973.38564.684-0.3388-1.34630.57660.72670.3007-0.2594-0.3770.01780.09610.66490.0122-0.08710.9153-0.25010.5421-0.273740.3728-7.4428
95.8719-1.34791.44082.3555-0.42364.9852-0.242-0.92060.56140.23950.16990.0419-0.3534-0.20280.09540.37070.0262-0.01140.6521-0.23690.475-9.743736.8382-14.714
103.65694.1918-3.69265.7564-2.38798.2779-0.035-0.2014-1.0240.0592-0.2721-0.7160.89330.40090.28810.34880.052-0.04080.44920.01790.58823.38043.3338-29.1549
113.59311.0983-0.48175.7405-2.41213.49190.099-0.2307-0.4707-0.0892-0.3154-0.76650.29030.47250.07360.37020.0467-0.03750.5352-0.08830.61969.8873.3938-26.7656
122.8705-0.15350.50272.2631-1.70042.55230.09220.2654-0.2422-0.19320.0312-0.18780.53360.0775-0.22970.4343-0.0302-0.01270.3961-0.10270.3912-3.92926.6165-37.1508
132.7056-1.07512.15363.7797-1.01583.52080.2546-0.2812-0.19250.033-0.19020.36210.1642-0.2733-0.1220.4108-0.1512-0.02440.5206-0.01350.4136-24.43578.162-40.8583
141.87010.1773-0.12261.7930.27331.3139-0.027-0.3433-0.11580.08530.04380.00240.0743-0.085-0.01910.2767-0.0163-0.02050.4564-0.02620.3198-6.599513.4837-24.7706
155.84082.4597-1.14214.2778-0.99612.0490.0424-0.513-0.460.2445-0.026-0.5450.17330.35580.00450.32590.0165-0.0810.5225-0.03820.400211.737310.3755-19.6254
166.0628-1.8961-0.18821.2976-0.46311.6601-0.0421-0.7845-0.13010.10270.23250.15390.0665-0.252-0.15750.3607-0.02540.01050.69690.02240.3707-20.743416.1347-11.9929
173.7936-0.494-4.1574.10021.12719.1452-0.1428-1.28660.44530.78590.09560.38460.0992-0.1626-0.00590.5810.01910.02360.933-0.12250.4623-18.210123.2928-2.1783
188.4384-2.56641.19143.60050.73882.6104-0.0541-0.7950.1880.5037-0.0203-0.08530.2041-0.3192-0.00470.4255-0.0324-0.00390.7785-0.09140.342-6.842721.5557-8.8173
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 1 THROUGH 17 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 18 THROUGH 33 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 34 THROUGH 52 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 53 THROUGH 67 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 68 THROUGH 187 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 188 THROUGH 217 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 218 THROUGH 240 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 241 THROUGH 257 )
9X-RAY DIFFRACTION9CHAIN 'A' AND (RESID 258 THROUGH 273 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 1 THROUGH 17 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 18 THROUGH 32 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 33 THROUGH 55 )
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 56 THROUGH 82 )
14X-RAY DIFFRACTION14CHAIN 'B' AND (RESID 83 THROUGH 187 )
15X-RAY DIFFRACTION15CHAIN 'B' AND (RESID 188 THROUGH 217 )
16X-RAY DIFFRACTION16CHAIN 'B' AND (RESID 218 THROUGH 240 )
17X-RAY DIFFRACTION17CHAIN 'B' AND (RESID 241 THROUGH 257 )
18X-RAY DIFFRACTION18CHAIN 'B' AND (RESID 258 THROUGH 273 )

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