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- PDB-1gg5: CRYSTAL STRUCTURE OF A COMPLEX OF HUMAN NAD[P]H-QUINONE OXIDOREDU... -

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Basic information

Entry
Database: PDB / ID: 1gg5
TitleCRYSTAL STRUCTURE OF A COMPLEX OF HUMAN NAD[P]H-QUINONE OXIDOREDUCTASE AND A CHEMOTHERAPEUTIC DRUG (E09) AT 2.5 A RESOLUTION
ComponentsNAD(P)H DEHYDROGENASE [QUINONE] 1
KeywordsOXIDOREDUCTASE / FLAVOPROTEIN / ROSSMANN FOLD
Function / homology
Function and homology information


response to L-glutamine / response to flavonoid / ubiquinone metabolic process / vitamin E metabolic process / vitamin K metabolic process / NAD(P)H dehydrogenase (quinone) / NADPH dehydrogenase (quinone) activity / 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 / NAD(P)H dehydrogenase (quinone) / NADPH dehydrogenase (quinone) activity / 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 carbohydrate / response to alkaloid / synaptic transmission, cholinergic / Regulation of ornithine decarboxylase (ODC) / negative regulation of ferroptosis / NFE2L2 regulating anti-oxidant/detoxification enzymes / response to amine / response to testosterone / superoxide dismutase activity / response to electrical stimulus / nitric oxide biosynthetic process / xenobiotic metabolic process / removal of superoxide radicals / response to hormone / cell redox homeostasis / response to nutrient / response to ischemia / protein catabolic process / negative regulation of protein catabolic process / cellular response to hydrogen peroxide / response to toxic substance / 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 / dendrite / synapse / 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
Chem-E09 / FLAVIN-ADENINE DINUCLEOTIDE / NAD(P)H dehydrogenase [quinone] 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.5 Å
AuthorsFaig, M. / Bianchet, M.A. / Winski, S. / Hargreaves, R. / Moody, C.J. / Hudnott, A.R. / Ross, D. / Amzel, L.M.
Citation
Journal: Structure / Year: 2001
Title: Structure-based development of anticancer drugs: complexes of NAD(P)H:quinone oxidoreductase 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.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Structures of Recombinant Human and Mouse Nad(P)H:Quinone Oxidoreductases: Species Comparison and Structural Changes with Substrate Binding and Release
Authors: Faig, M. / Bianchet, M.A. / Talalay, P. / Chen, S. / Winski, S. / Ross, D. / Amzel, L.M.
#2: Journal: BIOCHEM.SOC.TRANS. / Year: 1999
Title: Structure and Mechanism of Cytosolic Quinone Reductases
Authors: Bianchet, M.A. / Foster, C. / Faig, M. / Talalay, P. / Amzel, L.M.
#3: Journal: Biochemistry / Year: 1999
Title: Crystal Structure of Human Quinone Reductase Type 2, a Metalloprotein
Authors: Foster, C. / Bianchet, M.A. / Talalay, P. / Zhao, Q. / Amzel, L.M.
#4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1995
Title: The Three-Dimensional Structure of Nad(P)H:Quinone Reductase, a Flavoprotein Involved in Cancer Chemoprotection and Chemotherapy: Mechanism of Two-Electron Reduction
Authors: Li, R. / Bianchet, M.A. / Talalay, P. / Amzel, L.M.
History
DepositionJul 12, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 12, 2014Group: Structure summary
Revision 1.4Dec 27, 2023Group: 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)127,40912
Polymers123,1064
Non-polymers4,3038
Water1,874104
1
A: NAD(P)H DEHYDROGENASE [QUINONE] 1
C: NAD(P)H DEHYDROGENASE [QUINONE] 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7056
Polymers61,5532
Non-polymers2,1524
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9700 Å2
ΔGint-61 kcal/mol
Surface area20640 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)63,7056
Polymers61,5532
Non-polymers2,1524
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9660 Å2
ΔGint-60 kcal/mol
Surface area20620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.733, 55.454, 97.205
Angle α, β, γ (deg.)76.42, 77.22, 86.45
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
NAD(P)H DEHYDROGENASE [QUINONE] 1 / QUINONE REDUCTASE / DT-DIAPHORASE


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-E09 / 3-HYDROXYMETHYL-5-AZIRIDINYL-1METHYL-2-[1H-INDOLE-4,7-DIONE]-PROPANOL


Mass: 290.314 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H18N2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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 growMethod: vapor diffusion / pH: 8.5
Details: 30 % PEG 3350, 200 MM NAACETATE, 12-24 MICROM FAD, 100MM NA-TRICINE PH 8.5, pH 8.50, VAPOR DIFFUSION
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: 1.1
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Sep 19, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.2→43.44 Å / Num. obs: 46509 / % possible obs: 81.7 % / Observed criterion σ(I): -3 / Redundancy: 1.68 % / Biso Wilson estimate: 19.1 Å2 / Rsym value: 0.084 / Net I/σ(I): 4.79
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 1.39 % / Mean I/σ(I) obs: 1.4 / Rsym value: 0.169 / % possible all: 23.3
Reflection
*PLUS
Highest resolution: 2.5 Å / Num. obs: 38859 / Redundancy: 3.7 % / Rmerge(I) obs: 0.084
Reflection shell
*PLUS
% possible obs: 81.3 %

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Processing

Software
NameVersionClassification
CNS0.9refinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: OTHER / Resolution: 2.5→32.23 Å / Rfactor Rfree error: 0.005 / Data cutoff high rms absF: 402404.5 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.279 3679 10.3 %RANDOM
Rwork0.2 ---
obs0.2 35866 92.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 17.81 Å2 / ksol: 0.297 e/Å3
Displacement parametersBiso mean: 25 Å2
Baniso -1Baniso -2Baniso -3
1--6.37 Å2-5.93 Å2-0.75 Å2
2--3.62 Å24.95 Å2
3---2.76 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.5→32.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8692 0 296 104 9092
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_d22
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.221.5
X-RAY DIFFRACTIONc_mcangle_it2.012
X-RAY DIFFRACTIONc_scbond_it1.952
X-RAY DIFFRACTIONc_scangle_it2.972.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.351 540 10.5 %
Rwork0.281 4592 -
obs--79.3 %
Xplor file
Refine-IDSerial noTopol fileParam file
X-RAY DIFFRACTION1PROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA.TOP
X-RAY DIFFRACTION3WATER.TOP
X-RAY DIFFRACTION4ION.TOPWATER_REP.PARAM
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10.3 % / Rfactor obs: 0.2 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 25 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.351 / % reflection Rfree: 10.5 % / Rfactor Rwork: 0.281

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