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- PDB-1qbg: CRYSTAL STRUCTURE OF HUMAN DT-DIAPHORASE (NAD(P)H OXIDOREDUCTASE) -

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Basic information

Entry
Database: PDB / ID: 1qbg
TitleCRYSTAL STRUCTURE OF HUMAN DT-DIAPHORASE (NAD(P)H OXIDOREDUCTASE)
ComponentsNAD(P)H DEHYDROGENASE [QUINONE] 1
KeywordsOXIDOREDUCTASE / QUINONE / FAD / DT-DIAPHORASE
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
FLAVIN-ADENINE DINUCLEOTIDE / NAD(P)H dehydrogenase [quinone] 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsSkelly, J.V. / Sanderson, M.R. / Suter, D.A. / Baumann, U. / Gregory, D.S. / Bennett, M. / Hobbs, S.M. / Neidle, S.
CitationJournal: J.Med.Chem. / Year: 1999
Title: Crystal structure of human DT-diaphorase: a model for interaction with the cytotoxic prodrug 5-(aziridin-1-yl)-2,4-dinitrobenzamide (CB1954).
Authors: Skelly, J.V. / Sanderson, M.R. / Suter, D.A. / Baumann, U. / Read, M.A. / Gregory, D.S. / Bennett, M. / Hobbs, S.M. / Neidle, S.
History
DepositionApr 20, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 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)126,0208
Polymers122,8774
Non-polymers3,1424
Water00
1
A: NAD(P)H DEHYDROGENASE [QUINONE] 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5052
Polymers30,7191
Non-polymers7861
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NAD(P)H DEHYDROGENASE [QUINONE] 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5052
Polymers30,7191
Non-polymers7861
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: NAD(P)H DEHYDROGENASE [QUINONE] 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5052
Polymers30,7191
Non-polymers7861
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: NAD(P)H DEHYDROGENASE [QUINONE] 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5052
Polymers30,7191
Non-polymers7861
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
C: NAD(P)H DEHYDROGENASE [QUINONE] 1
D: NAD(P)H DEHYDROGENASE [QUINONE] 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0104
Polymers61,4392
Non-polymers1,5712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8190 Å2
ΔGint-48 kcal/mol
Surface area21500 Å2
MethodPISA, PQS
6
A: NAD(P)H DEHYDROGENASE [QUINONE] 1
B: NAD(P)H DEHYDROGENASE [QUINONE] 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0104
Polymers61,4392
Non-polymers1,5712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8290 Å2
ΔGint-47 kcal/mol
Surface area21370 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)55.88, 57.49, 98.77
Angle α, β, γ (deg.)77.1, 76.2, 86.9
Int Tables number1
Cell settingtriclinic
Space group name H-MP1

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Components

#1: Protein
NAD(P)H DEHYDROGENASE [QUINONE] 1 / E.C.1.6.99.2 / DT-DIAPHORASE (NAD(P)H OXIDOREDUCTASE (QUINONE) / QUINONE REDUCTASE / DT-DIAPHORASE / DTD / NAD(P)H ...DT-DIAPHORASE (NAD(P)H OXIDOREDUCTASE (QUINONE) / QUINONE REDUCTASE / DT-DIAPHORASE / DTD / NAD(P)H menadione oxidoreductase 1 / dioxin-inducible


Mass: 30719.365 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

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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: 2.44 Å3/Da / Density % sol: 49.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Sitting drop, PEG4000, CYMAL-3 detergent, sodium phosphate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal
*PLUS
Density % sol: 47 %
Crystal grow
*PLUS
Temperature: 18 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
19.7 mg/mlprotein1drop
2100 mMsodium phosphate1drop
325 %(w/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Oct 15, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. all: 47496 / Num. obs: 43746 / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Rmerge(I) obs: 0.132 / Net I/σ(I): 4.98
Reflection shellResolution: 2.3→2.4 Å / Rmerge(I) obs: 0.6 / Num. unique all: 4439 / % possible all: 70
Reflection
*PLUS
% possible obs: 81.5 % / Num. measured all: 193332

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
SCALEPACKdata scaling
RefinementResolution: 2.3→40 Å / Cross valid method: THROUGHOUT / σ(F): 4 / σ(I): 2 / Stereochemistry target values: Engh & Huber / Details: used x-plor procedure
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1867 4.3 %random
all0.238 47496 --
obs0.232 43746 --
Refinement stepCycle: LAST / Resolution: 2.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8669 0 212 0 8881
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 40 Å / % reflection Rfree: 4.3 % / Rfactor Rfree: 0.28 / Rfactor Rwork: 0.232
Solvent computation
*PLUS
Displacement parameters
*PLUS

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