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- PDB-3ox1: X-ray Structural study of quinone reductase II inhibition by comp... -

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Basic information

Entry
Database: PDB / ID: 3ox1
TitleX-ray Structural study of quinone reductase II inhibition by compounds with micromolar to nanomolar range IC50 values
ComponentsRibosyldihydronicotinamide dehydrogenase [quinone]
KeywordsOXIDOREDUCTASE / QR2 / NQ02 / FLAVOPROTEIN / METAL-2 BINDING / PHOSPHOPROTEIN / FAD
Function / homology
Function and homology information


ribosyldihydronicotinamide dehydrogenase (quinone) / dihydronicotinamide riboside quinone reductase activity / quinone catabolic process / resveratrol binding / oxidoreductase activity, acting on other nitrogenous compounds as donors / melatonin binding / NAD(P)H dehydrogenase (quinone) activity / Phase I - Functionalization of compounds / chloride ion binding / FAD binding ...ribosyldihydronicotinamide dehydrogenase (quinone) / dihydronicotinamide riboside quinone reductase activity / quinone catabolic process / resveratrol binding / oxidoreductase activity, acting on other nitrogenous compounds as donors / melatonin binding / NAD(P)H dehydrogenase (quinone) activity / Phase I - Functionalization of compounds / chloride ion binding / FAD binding / electron transfer activity / oxidoreductase activity / protein homodimerization activity / extracellular exosome / zinc ion binding / nucleoplasm / 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-695 / FLAVIN-ADENINE DINUCLEOTIDE / Ribosyldihydronicotinamide dehydrogenase [quinone]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsPegan, S.D. / Sturdy, M. / Ferry, G. / Delagrange, P. / Boutin, J.A. / Mesecar, A.D.
CitationJournal: Protein Sci. / Year: 2011
Title: X-ray structural studies of quinone reductase 2 nanomolar range inhibitors.
Authors: Pegan, S.D. / Sturdy, M. / Ferry, G. / Delagrange, P. / Boutin, J.A. / Mesecar, A.D.
History
DepositionSep 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _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: Ribosyldihydronicotinamide dehydrogenase [quinone]
B: Ribosyldihydronicotinamide dehydrogenase [quinone]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2768
Polymers51,9612
Non-polymers2,3156
Water7,782432
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7380 Å2
ΔGint-31 kcal/mol
Surface area17940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.587, 83.741, 106.432
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ribosyldihydronicotinamide dehydrogenase [quinone] / NRH dehydrogenase [quinone] 2 / NRH:quinone oxidoreductase 2 / Quinone reductase 2 / QR2


Mass: 25980.533 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NQO2, NMOR2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P16083, EC: 1.10.99.2
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-695 / N-{2-[7-(methylsulfamoyl)naphthalen-1-yl]ethyl}acetamide


Mass: 306.380 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H18N2O3S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 432 / 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: 2.43 Å3/Da / Density % sol: 49.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 1.3 M ammonium sulfate, 0.1 M Bis-Tris, 0.1 M NaCl, 5 mM DTT, 12 M FAD, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 13, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→65.8 Å / Num. all: 34979 / Num. obs: 33965 / % possible obs: 97.1 %
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.062 / % possible all: 95.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→65.8 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.2036 / WRfactor Rwork: 0.1592 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.8535 / SU B: 3.803 / SU ML: 0.107 / SU R Cruickshank DPI: 0.1884 / SU Rfree: 0.1668 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2243 1709 5 %RANDOM
Rwork0.1748 ---
obs0.1773 33915 96.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.72 Å2 / Biso mean: 20.8321 Å2 / Biso min: 4.33 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å2-0 Å2-0 Å2
2--0.62 Å20 Å2
3----1.37 Å2
Refinement stepCycle: LAST / Resolution: 2→65.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3628 0 150 432 4210
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223897
X-RAY DIFFRACTIONr_angle_refined_deg1.3061.9885314
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2765457
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.16924.186172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.00415611
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7461516
X-RAY DIFFRACTIONr_chiral_restr0.0860.2560
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212958
X-RAY DIFFRACTIONr_mcbond_it0.6471.52276
X-RAY DIFFRACTIONr_mcangle_it1.19823669
X-RAY DIFFRACTIONr_scbond_it1.72831621
X-RAY DIFFRACTIONr_scangle_it2.8034.51645
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 101 -
Rwork0.198 2283 -
all-2384 -
obs--93.93 %

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