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- PDB-1kbq: Complex of Human NAD(P)H quinone Oxidoreductase with 5-methoxy-1,... -

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Basic information

Entry
Database: PDB / ID: 1kbq
TitleComplex of Human NAD(P)H quinone Oxidoreductase with 5-methoxy-1,2-dimethyl-3-(4-nitrophenoxymethyl)indole-4,7-dione (ES936)
ComponentsNAD(P)H dehydrogenase [quinone] 1
KeywordsOXIDOREDUCTASE / FLAVOENZYME / PRODRUG-ENZYME COMPLEX
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 / cellular response to oxidative stress / 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-936 / FLAVIN-ADENINE DINUCLEOTIDE / NAD(P)H dehydrogenase [quinone] 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER / Resolution: 1.8 Å
AuthorsFaig, M. / Bianchet, M.A. / Amzel, L.M.
Citation
Journal: Biochemistry / Year: 2001
Title: Characterization of a mechanism-based inhibitor of NAD(P)H:quinone oxidoreductase 1 by biochemical, X-ray crystallographic, and mass spectrometric approaches.
Authors: Winski, S.L. / Faig, M. / Bianchet, M.A. / Siegel, D. / Swann, E. / Fung, K. / Duncan, M.W. / Moody, C.J. / Amzel, L.M. / Ross, D.
#1: Journal: Structure / Year: 2001
Title: Structure-based Development of Anticancer Drugs: Complexes of NAD(P)H:Quinone Reductase 1 with Chemotherapeutic Quinones
Authors: Faig, M. / Bianchet, M.A. / Winski, S. / Hargreaves, R. / Moody, C.J. / Hudnott, A.R. / Ross, D. / Amzel, L.M.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Structures of Recombinant Mouse and Human NAD(P)H:Quinone Oxidoreductases: Species Comparison and Structural Changes with Substrate Binding and Release
Authors: Faig, M. / Bianchet, M.A. / Chen, S. / Winski, S.L. / Ross, D. / Talalay, P. / Amzel, L.M.
History
DepositionNov 6, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,67312
Polymers123,1064
Non-polymers4,5688
Water9,260514
1
A: NAD(P)H dehydrogenase [quinone] 1
C: NAD(P)H dehydrogenase [quinone] 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8376
Polymers61,5532
Non-polymers2,2844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9990 Å2
ΔGint-62 kcal/mol
Surface area20540 Å2
MethodPISA
2
B: NAD(P)H dehydrogenase [quinone] 1
D: NAD(P)H dehydrogenase [quinone] 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8376
Polymers61,5532
Non-polymers2,2844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9920 Å2
ΔGint-65 kcal/mol
Surface area20490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.480, 56.772, 96.907
Angle α, β, γ (deg.)77.25, 76.83, 86.90
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 30776.412 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P15559, EC: 1.6.99.2
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-936 / 5-METHOXY-1,2-DIMETHYL-3-(4-NITROPHENOXYMETHYL)INDOLE-4,7-DIONE


Mass: 356.329 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H16N2O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 514 / 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: 2.35 Å3/Da / Density % sol: 47.74 %
Crystal growpH: 8.5 / Details: pH 8.5
Crystal grow
*PLUS
Temperature: 25 ℃ / pH: 8 / Method: vapor diffusion, hanging drop / Details: Faig, M., (2000) Proc.Natl.Acad.Sci.USA, 97, 3177.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110-15 mg/mlprotein1drop
225 mMTris-HCl1drop
30.005 mMFAD1drop
430 %PEG33501reservoir
5200 mMsodium acetate1reservoir
6100 mg/mlsodium tricine1reservoir
70.012-0.024 mMFAD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Sep 24, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 103269 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 18.2 Å2 / Rsym value: 0.096
Reflection shellResolution: 1.8→1.86 Å / % possible obs: 85.3 % / Mean I/σ(I) obs: 1 / Rsym value: 0.323 / % possible all: 85.3
Reflection
*PLUS
Redundancy: 3.4 % / Rmerge(I) obs: 0.096
Reflection shell
*PLUS
% possible obs: 85 %

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER
Starting model: 1AD4

1ad4


Resolution: 1.8→32.19 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 355979.16 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.252 7743 7.9 %RANDOM
Rwork0.215 ---
obs-98527 94.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.4385 Å2 / ksol: 0.325222 e/Å3
Displacement parametersBiso mean: 25.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å2-1.27 Å23.59 Å2
2---0.42 Å23.15 Å2
3---0.89 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 1.8→32.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8664 0 316 514 9494
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.981.5
X-RAY DIFFRACTIONc_mcangle_it1.672
X-RAY DIFFRACTIONc_scbond_it1.532
X-RAY DIFFRACTIONc_scangle_it2.382.5
LS refinement shellResolution: 1.8→1.91 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rwork0.33 13933 -
obs--80.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2fad_xplor.parDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5936.PAR
Software
*PLUS
Name: CNS / Version: 1.1 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 99339 / σ(F): 0 / % reflection Rfree: 7.9 % / Rfactor obs: 0.215 / Rfactor Rfree: 0.257
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 25.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.39
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.82
X-RAY DIFFRACTIONc_mcbond_it0.981.5
X-RAY DIFFRACTIONc_scbond_it1.532
X-RAY DIFFRACTIONc_mcangle_it1.672
X-RAY DIFFRACTIONc_scangle_it2.382.5
LS refinement shell
*PLUS
Rfactor Rwork: 0.33

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