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- PDB-1kbo: Complex of Human recombinant NAD(P)H:Quinone Oxide reductase type... -

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Basic information

Entry
Database: PDB / ID: 1kbo
TitleComplex of Human recombinant NAD(P)H:Quinone Oxide reductase type 1 with 5-methoxy-1,2-dimethyl-3-(phenoxymethyl)indole-4,7-dione (ES1340)
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 / vitamin K metabolic process / cytochrome-b5 reductase activity, acting on NAD(P)H / 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 / vitamin K metabolic process / cytochrome-b5 reductase activity, acting on NAD(P)H / 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 lipopolysaccharide / response to oxidative stress / innate immune response / synapse / 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
Chem-340 / FLAVIN-ADENINE DINUCLEOTIDE / NAD(P)H dehydrogenase [quinone] 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.3 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 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)127,49312
Polymers123,1064
Non-polymers4,3888
Water2,972165
1
A: NAD(P)H dehydrogenase [quinone] 1
C: NAD(P)H dehydrogenase [quinone] 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7476
Polymers61,5532
Non-polymers2,1944
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9760 Å2
ΔGint-54 kcal/mol
Surface area20750 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)63,7476
Polymers61,5532
Non-polymers2,1944
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9830 Å2
ΔGint-58 kcal/mol
Surface area20810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.636, 57.026, 96.878
Angle α, β, γ (deg.)76.80, 76.93, 86.28
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-340 / 5-METHOXY-1,2-DIMETHYL-3-(PHENOXYMETHYL)INDOLE-4,7-DIONE


Mass: 311.332 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H17NO4
#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.37 Å3/Da / Density % sol: 48.03 %
Crystal growTemperature: 293 K / pH: 8.5 / Details: PEG 4K, Na Acetate, pH 8.5, temperature 293K
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: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 1, 1999 / Details: OSMIC MIRRORS
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→35.5 Å / Num. obs: 47881 / % possible obs: 96.5 % / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Biso Wilson estimate: 21.2 Å2 / Rsym value: 0.098 / Net I/σ(I): 13.57
Reflection shellResolution: 2.3→2.38 Å / Mean I/σ(I) obs: 1.7 / Rsym value: 0.221 / % possible all: 94.3
Reflection
*PLUS
Rmerge(I) obs: 0.098
Reflection shell
*PLUS
% possible obs: 94.3 %

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Processing

Software
NameVersionClassification
CCP4model building
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.3→35.55 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 461040.1 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.287 3825 10.2 %RANDOM
Rwork0.2 ---
all0.232 ---
obs0.2071 37344 74.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.7923 Å2 / ksol: 0.305857 e/Å3
Displacement parametersBiso mean: 32.9 Å2
Baniso -1Baniso -2Baniso -3
1-5.29 Å2-1.53 Å21.4 Å2
2---1.41 Å23.61 Å2
3----3.88 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.3→35.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8700 0 304 165 9169
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_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.21.5
X-RAY DIFFRACTIONc_mcangle_it0.372
X-RAY DIFFRACTIONc_scbond_it0.152
X-RAY DIFFRACTIONc_scangle_it0.262.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.341 334 9.9 %
Rwork0.278 3052 -
obs--40.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2NEWFAD_Xplor.parDNA-RNA.TOP
X-RAY DIFFRACTION3340.PARWATER.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 1.1 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 10.2 % / Rfactor obs: 0.204 / Rfactor Rfree: 0.286 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 32.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83
X-RAY DIFFRACTIONc_mcbond_it0.21.5
X-RAY DIFFRACTIONc_scbond_it0.152
X-RAY DIFFRACTIONc_mcangle_it0.372
X-RAY DIFFRACTIONc_scangle_it0.262.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.341 / % reflection Rfree: 9.9 % / Rfactor Rwork: 0.278

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