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- PDB-5eai: Crystal Structure of NAD(P)H dehydrogenase, quinone 1 complexed w... -

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Basic information

Entry
Database: PDB / ID: 5eai
TitleCrystal Structure of NAD(P)H dehydrogenase, quinone 1 complexed with a chemotherapeutic naphthoquinone E6a
ComponentsNAD(P)H dehydrogenase [quinone] 1
KeywordsOXIDOREDUCTASE / NQO1 / two-electron reduction of Quinone / NAD(P)H dehydrogenase / dimeric naphthoquinone
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) / negative regulation of ferroptosis / NFE2L2 regulating anti-oxidant/detoxification enzymes / response to testosterone / response to amine / superoxide dismutase activity / response to nutrient / response to electrical stimulus / nitric oxide biosynthetic process / xenobiotic metabolic process / removal of superoxide radicals / response to hormone / cell redox homeostasis / response to ischemia / negative regulation of protein catabolic process / 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 / Flavodoxin domain / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-E6A / FLAVIN-ADENINE DINUCLEOTIDE / NAD(P)H dehydrogenase [quinone] 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsPidugu, L.S. / Mbimba, J.E. / Ahmad, M. / Pozharski, E. / Sausville, E.A. / Emadi, A. / Toth, E.A.
CitationJournal: Bmc Struct.Biol. / Year: 2016
Title: A direct interaction between NQO1 and a chemotherapeutic dimeric naphthoquinone.
Authors: Pidugu, L.S. / Mbimba, J.C. / Ahmad, M. / Pozharski, E. / Sausville, E.A. / Emadi, A. / Toth, E.A.
History
DepositionOct 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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
E: NAD(P)H dehydrogenase [quinone] 1
F: NAD(P)H dehydrogenase [quinone] 1
G: NAD(P)H dehydrogenase [quinone] 1
H: NAD(P)H dehydrogenase [quinone] 1
I: NAD(P)H dehydrogenase [quinone] 1
J: NAD(P)H dehydrogenase [quinone] 1
K: NAD(P)H dehydrogenase [quinone] 1
L: NAD(P)H dehydrogenase [quinone] 1
M: NAD(P)H dehydrogenase [quinone] 1
N: NAD(P)H dehydrogenase [quinone] 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)449,86333
Polymers436,79914
Non-polymers13,06419
Water90150
1
A: NAD(P)H dehydrogenase [quinone] 1
B: NAD(P)H dehydrogenase [quinone] 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3845
Polymers62,4002
Non-polymers1,9843
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8410 Å2
ΔGint-52 kcal/mol
Surface area21760 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)63,9714
Polymers62,4002
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8240 Å2
ΔGint-53 kcal/mol
Surface area22170 Å2
MethodPISA
3
E: NAD(P)H dehydrogenase [quinone] 1
F: NAD(P)H dehydrogenase [quinone] 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3845
Polymers62,4002
Non-polymers1,9843
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8570 Å2
ΔGint-52 kcal/mol
Surface area21880 Å2
MethodPISA
4
G: NAD(P)H dehydrogenase [quinone] 1
H: NAD(P)H dehydrogenase [quinone] 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3845
Polymers62,4002
Non-polymers1,9843
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8130 Å2
ΔGint-53 kcal/mol
Surface area22170 Å2
MethodPISA
5
I: NAD(P)H dehydrogenase [quinone] 1
J: NAD(P)H dehydrogenase [quinone] 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9714
Polymers62,4002
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8110 Å2
ΔGint-53 kcal/mol
Surface area22450 Å2
MethodPISA
6
K: NAD(P)H dehydrogenase [quinone] 1
L: NAD(P)H dehydrogenase [quinone] 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3845
Polymers62,4002
Non-polymers1,9843
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8170 Å2
ΔGint-53 kcal/mol
Surface area22250 Å2
MethodPISA
7
M: NAD(P)H dehydrogenase [quinone] 1
N: NAD(P)H dehydrogenase [quinone] 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3845
Polymers62,4002
Non-polymers1,9843
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8200 Å2
ΔGint-53 kcal/mol
Surface area21480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.600, 210.770, 228.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 31199.922 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NQO1, DIA4, NMOR1 / Plasmid: 19-PPS
Details (production host): pET19b with a prescission protease cleave site inserted
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


Mass: 785.550 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-E6A / (2~{R},3~{R})-2-[(2~{S},3~{S})-3-bromanyl-1,4-bis(oxidanylidene)-2,3-dihydronaphthalen-2-yl]-3-oxidanyl-2,3-dihydronaphthalene-1,4-dione


Mass: 413.218 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C20H13BrO5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.14 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG3350, sodium potassium tartarate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→95.67 Å / Num. obs: 102839 / Biso Wilson estimate: 71.98 Å2 / Rsym value: 0.116

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→95.67 Å / Cor.coef. Fo:Fc: 0.9173 / Cor.coef. Fo:Fc free: 0.8995 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.338
RfactorNum. reflection% reflectionSelection details
Rfree0.22 4972 4.84 %RANDOM
Rwork0.1832 ---
obs0.185 102741 99.94 %-
Displacement parametersBiso mean: 73.27 Å2
Baniso -1Baniso -2Baniso -3
1--0.3211 Å20 Å20 Å2
2--23.9954 Å20 Å2
3----23.6743 Å2
Refine analyzeLuzzati coordinate error obs: 0.422 Å
Refinement stepCycle: LAST / Resolution: 2.9→95.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30099 0 872 50 31021
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0131861HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1343245HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d10882SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes692HARMONIC2
X-RAY DIFFRACTIONt_gen_planes5076HARMONIC5
X-RAY DIFFRACTIONt_it31861HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.92
X-RAY DIFFRACTIONt_other_torsion19.65
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion4017SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact36113SEMIHARMONIC4
LS refinement shellResolution: 2.9→2.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3025 354 4.72 %
Rwork0.2517 7147 -
all0.254 7501 -
obs--99.94 %
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)
11.2454-0.0063-0.14243.2934-0.12720.9450.1313-0.11250.08290.2615-0.08210.0054-0.07160.1029-0.04930.1005-0.0719-0.0039-0.0915-0.0653-0.2035-24.201417.6576-17.7094
21.050.5846-0.28383.61450.01551.39210.02780.07690.2098-0.59540.01840.7223-0.0151-0.0747-0.04620.05140.0263-0.123-0.1889-0.0065-0.0514-39.562417.5495-33.4547
31.9160.3897-0.31543.95680.12681.57810.10410.08570.2108-0.2257-0.11930.17380.1975-0.14210.0152-0.06950.0039-0.0379-0.047-0.0087-0.1951-62.546316.517-95.2298
41.9090.0633-0.55382.9772-0.16391.15330.1465-0.25860.1660.5759-0.1825-0.56240.09170.2140.036-0.0438-0.0513-0.0869-0.0677-0.0125-0.0874-46.997118.6646-79.5326
52.12110.29970.25763.7332-0.16531.2369-0.18990.1845-0.0869-0.35130.04140.2803-0.21120.0940.1485-0.1579-0.0481-0.0341-0.0941-0.0107-0.0337-37.197-25.7305-32.0649
62.0250.05880.18152.6054-0.15971.24560.0234-0.4103-0.10210.6274-0.09990.1474-0.0946-0.1220.0765-0.0629-0.06130.0642-0.07620.0627-0.0666-38.79-28.7434-10.2233
73.5157-0.8413-0.02782.375-0.72011.55950.09580.6459-0.1266-0.524-0.18180.07390.28540.07930.0860.00460.12780.0524-0.02710.0455-0.2484-18.1152-41.2276-99.2691
83.5966-1.27650.1614.1066-0.48530.8173-0.1259-0.42520.11290.16060.10130.1938-0.13910.13190.0246-0.0710.04970.1099-0.02260.0833-0.2473-16.0091-38.2563-77.4003
91.73050.31860.11063.1027-0.17121.0279-0.0393-0.2191-0.14040.2983-0.10590.11740.0847-0.07870.14520.0034-0.00680.0005-0.1050.0497-0.1078-64.7774-27.4821-77.3152
101.69870.07480.07072.4506-0.24861.1647-0.07230.1624-0.0742-0.4131-0.05070.24250.06030.07950.1230.05520.0282-0.0334-0.13610.0112-0.0972-62.8643-26.7078-99.4624
113.193-0.18670.0513.20460.28661.3401-0.03630.6861-0.1789-0.5333-0.0039-0.2236-0.03-0.10670.0401-0.1264-0.05060.1094-0.0019-0.0656-0.1638-85.8517-36.3897-34.2076
123.4401-0.0622-0.10692.4575-0.02331.78-0.1119-0.1922-0.47310.1532-0.0493-0.10880.2670.02850.1612-0.2225-0.07430.0467-0.16190.07450.0535-84.0691-42.2403-12.8779
132.89920.2362-1.09621.23160.20342.14740.14120.40510.2294-0.39920.00780.1954-0.1014-0.271-0.14890.03490.02490.0545-0.1085-0.0524-0.1206-96.952430.6015-65.6165
141.9887-0.4993-0.90932.80261.19082.24060.0943-0.51130.08420.14780.2202-0.45720.09940.2375-0.3145-0.0902-0.04240.057-0.0466-0.1272-0.1202-83.803528.7339-47.9494
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|3 - A|272 A|601 - A|601 }A3 - 272
2X-RAY DIFFRACTION1{ A|3 - A|272 A|601 - A|601 }A601
3X-RAY DIFFRACTION2{ B|3 - B|272 B|301 - B|301 }B3 - 272
4X-RAY DIFFRACTION2{ B|3 - B|272 B|301 - B|301 }B301
5X-RAY DIFFRACTION3{ C|1 - C|272 C|601 - C|601 }C1 - 272
6X-RAY DIFFRACTION3{ C|1 - C|272 C|601 - C|601 }C601
7X-RAY DIFFRACTION4{ D|3 - D|273 D|301 - D|301 }D3 - 273
8X-RAY DIFFRACTION4{ D|3 - D|273 D|301 - D|301 }D301
9X-RAY DIFFRACTION5{ E|2 - E|272 E|601 - E|601 }E2 - 272
10X-RAY DIFFRACTION5{ E|2 - E|272 E|601 - E|601 }E601
11X-RAY DIFFRACTION6{ F|2 - F|272 F|301 - F|301 }F2 - 272
12X-RAY DIFFRACTION6{ F|2 - F|272 F|301 - F|301 }F301
13X-RAY DIFFRACTION7{ G|1 - G|272 G|601 - G|601 }G1 - 272
14X-RAY DIFFRACTION7{ G|1 - G|272 G|601 - G|601 }G601
15X-RAY DIFFRACTION8{ H|2 - H|272 H|301 - H|301 }H2 - 272
16X-RAY DIFFRACTION8{ H|2 - H|272 H|301 - H|301 }H301
17X-RAY DIFFRACTION9{ I|1 - I|272 I|601 - I|601 }I1 - 272
18X-RAY DIFFRACTION9{ I|1 - I|272 I|601 - I|601 }I601
19X-RAY DIFFRACTION10{ J|2 - J|272 J|301 - J|301 }J2 - 272
20X-RAY DIFFRACTION10{ J|2 - J|272 J|301 - J|301 }J301
21X-RAY DIFFRACTION11{ K|2 - K|272 K|601 - K|601 }K2 - 272
22X-RAY DIFFRACTION11{ K|2 - K|272 K|601 - K|601 }K601
23X-RAY DIFFRACTION12{ L|1 - L|273 L|301 - L|301 }L1 - 273
24X-RAY DIFFRACTION12{ L|1 - L|273 L|301 - L|301 }L301
25X-RAY DIFFRACTION13{ M|1 - M|273 M|601 - M|601 }M1 - 273
26X-RAY DIFFRACTION13{ M|1 - M|273 M|601 - M|601 }M601
27X-RAY DIFFRACTION14{ N|2 - N|272 N|301 - N|301 }N2 - 272
28X-RAY DIFFRACTION14{ N|2 - N|272 N|301 - N|301 }N301

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