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- PDB-3jsx: X-ray Crystal structure of NAD(P)H: Quinone Oxidoreductase-1 (NQO... -

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Basic information

Entry
Database: PDB / ID: 3jsx
TitleX-ray Crystal structure of NAD(P)H: Quinone Oxidoreductase-1 (NQO1) bound to the coumarin-based inhibitor AS1
ComponentsNAD(P)H dehydrogenase [quinone] 1
KeywordsOXIDOREDUCTASE / coumarin-based inhibitors / NQ01 / FAD / Flavoprotein / NAD / NADP
Function / homology
Function and homology information


ubiquinone metabolic process / vitamin E metabolic process / NAD(P)H dehydrogenase (quinone) / NADPH dehydrogenase (quinone) activity / cytochrome-b5 reductase activity, acting on NAD(P)H / vitamin K metabolic process / NADH dehydrogenase (quinone) (non-electrogenic) activity / NAD(P)H dehydrogenase (quinone) activity / synaptic transmission, cholinergic / Regulation of ornithine decarboxylase (ODC) ...ubiquinone metabolic process / vitamin E metabolic process / NAD(P)H dehydrogenase (quinone) / NADPH dehydrogenase (quinone) activity / cytochrome-b5 reductase activity, acting on NAD(P)H / vitamin K metabolic process / NADH dehydrogenase (quinone) (non-electrogenic) activity / NAD(P)H dehydrogenase (quinone) activity / synaptic transmission, cholinergic / Regulation of ornithine decarboxylase (ODC) / NFE2L2 regulating anti-oxidant/detoxification enzymes / negative regulation of ferroptosis / nitric oxide biosynthetic process / xenobiotic metabolic process / removal of superoxide radicals / cell redox homeostasis / protein catabolic process / negative regulation of protein catabolic process / response to toxic substance / protein polyubiquitination / response to oxidative stress / cellular response to oxidative stress / response to lipopolysaccharide / innate immune response / synapse / 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-CC2 / FLAVIN-ADENINE DINUCLEOTIDE / NAD(P)H dehydrogenase [quinone] 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsDunstan, M.S. / Levy, C. / Leys, D.
CitationJournal: J.Med.Chem. / Year: 2009
Title: Synthesis and biological evaluation of coumarin-based inhibitors of NAD(P)H: quinone oxidoreductase-1 (NQO1).
Authors: Nolan, K.A. / Doncaster, J.R. / Dunstan, M.S. / Scott, K.A. / Frenkel, A.D. / Siegel, D. / Ross, D. / Barnes, J. / Levy, C. / Leys, D. / Whitehead, R.C. / Stratford, I.J. / Bryce, R.A.
History
DepositionSep 11, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 10, 2014Group: Structure summary
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)255,13924
Polymers246,2118
Non-polymers8,92716
Water7,819434
1
A: NAD(P)H dehydrogenase [quinone] 1
B: NAD(P)H dehydrogenase [quinone] 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7856
Polymers61,5532
Non-polymers2,2324
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8680 Å2
ΔGint-50 kcal/mol
Surface area21390 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)63,7856
Polymers61,5532
Non-polymers2,2324
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8740 Å2
ΔGint-52 kcal/mol
Surface area21380 Å2
MethodPISA
3
E: NAD(P)H dehydrogenase [quinone] 1
G: NAD(P)H dehydrogenase [quinone] 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7856
Polymers61,5532
Non-polymers2,2324
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8630 Å2
ΔGint-46 kcal/mol
Surface area21450 Å2
MethodPISA
4
F: NAD(P)H dehydrogenase [quinone] 1
H: NAD(P)H dehydrogenase [quinone] 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7856
Polymers61,5532
Non-polymers2,2324
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8730 Å2
ΔGint-49 kcal/mol
Surface area21450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.040, 209.940, 102.080
Angle α, β, γ (deg.)90.00, 109.93, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 30776.412 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DIA4, NMOR1, NQO1, NQO1 cDNA / Plasmid: PKK 233-2 / 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.: 8 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-CC2 / 4-hydroxy-6,7-dimethyl-3-(naphthalen-1-ylmethyl)-2H-chromen-2-one


Mass: 330.377 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C22H18O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 434 / 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: 2.87 Å3/Da / Density % sol: 57.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 2.4M ammonium sulfate, 0.1M Tris buffer pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 9, 2009
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.45→47.954 Å / Num. all: 107399 / Num. obs: 100053 / % possible obs: 93.2 % / Observed criterion σ(F): 1.99 / Observed criterion σ(I): 1.99 / Redundancy: 4.1 % / Biso Wilson estimate: 53.46 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.079 / Net I/σ(I): 13.98
Reflection shellResolution: 2.45→2.51 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 2.8 / Num. unique all: 6558 / % possible all: 84.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2F1O

2f1o


Resolution: 2.45→47.954 Å / SU ML: 0.15 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.99 / σ(I): 2 / Phase error: 33.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.269 5063 5.01 %Random
Rwork0.2063 ---
obs0.2095 100053 99.66 %-
all-101037 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.469 Å2 / ksol: 0.334 e/Å3
Displacement parametersBiso mean: 53.6 Å2
Baniso -1Baniso -2Baniso -3
1-30.0319 Å20 Å2-2.4046 Å2
2---11.673 Å20 Å2
3----18.3588 Å2
Refine analyzeLuzzati coordinate error obs: 0.15 Å
Refinement stepCycle: LAST / Resolution: 2.45→47.954 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17176 0 624 434 18234
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00818328
X-RAY DIFFRACTIONf_angle_d1.27824880
X-RAY DIFFRACTIONf_dihedral_angle_d19.5126536
X-RAY DIFFRACTIONf_chiral_restr0.0792576
X-RAY DIFFRACTIONf_plane_restr0.0053072
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.45-2.47780.40931540.297311897
2.4778-2.5070.34481750.2785313898
2.507-2.53760.34851660.27513219100
2.5376-2.56970.36751570.27413182100
2.5697-2.60350.35581750.27343209100
2.6035-2.63920.35481740.25923211100
2.6392-2.67690.36511700.2723190100
2.6769-2.71680.3311560.26963194100
2.7168-2.75930.36531550.26533232100
2.7593-2.80450.34351550.26463223100
2.8045-2.85280.3461860.27163172100
2.8528-2.90470.38621470.27553241100
2.9047-2.96060.32421550.26393184100
2.9606-3.0210.33851680.25153223100
3.021-3.08670.32181630.25293199100
3.0867-3.15850.33521460.24223211100
3.1585-3.23740.29871760.2333183100
3.2374-3.32490.3091880.22323205100
3.3249-3.42280.26911880.22243156100
3.4228-3.53320.2781670.21093226100
3.5332-3.65940.2851880.20193188100
3.6594-3.80590.23711610.18453183100
3.8059-3.9790.24861730.1743181100
3.979-4.18870.19891640.18033246100
4.1887-4.4510.24581810.15983221100
4.451-4.79430.20511630.1553169100
4.7943-5.27630.22111920.15473229100
5.2763-6.03850.22371660.18583205100
6.0385-7.60290.22791780.18573204100
7.6029-47.96310.23391760.185323299

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