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Basic information

Entry
Database: PDB / ID: 3nhk
TitleX-ray Crystallographic Structure Activity Relationship (SAR) of Casimiroin and its Analogs Bound to Human Quinone Reductase 2
ComponentsRibosyldihydronicotinamide dehydrogenase [quinone]
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / protein dimer / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
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
FLAVIN-ADENINE DINUCLEOTIDE / 6,7,8-trimethoxy-1,4-dimethylquinolin-2(1H)-one / Ribosyldihydronicotinamide dehydrogenase [quinone]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.96 Å
AuthorsSturdy, M.
Citation
Journal: To be Published
Title: X-ray Crystallographic Structure Activity Relationship (SAR) of Casimiroin and its Analogs Bound to Human Quinone Reductase 2
Authors: Sturdy, M.
#1: Journal: J.Med.Chem. / Year: 2009
Title: Synthesis of casimiroin and optimization of its quinone reductase 2 and aromatase inhibitory activities.
Authors: Maiti, A. / Reddy, P.V. / Sturdy, M. / Marler, L. / Pegan, S.D. / Mesecar, A.D. / Pezzuto, J.M. / Cushman, M.
History
DepositionJun 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_auth_seq_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)53,9278
Polymers51,6992
Non-polymers2,2286
Water6,936385
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7100 Å2
ΔGint-32 kcal/mol
Surface area18380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.751, 83.661, 106.513
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: 25849.338 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NQO2, NMOR2 / Plasmid: pET-23d / 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


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-VAP / 6,7,8-trimethoxy-1,4-dimethylquinolin-2(1H)-one


Mass: 263.289 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H17NO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / 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: 2.45 Å3/Da / Density % sol: 49.7 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 6.7
Details: 1.339 M ammonium sulfate, 0.1 M Bis-Tris, 0.1 M NaCl, 5 mM DTT, 12 uM FAD, pH 6.7, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 15, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 5.9 % / Av σ(I) over netI: 12.03 / Number: 203461 / Rmerge(I) obs: 0.126 / Χ2: 0.97 / D res high: 1.97 Å / D res low: 50 Å / Num. obs: 34689 / % possible obs: 93.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.245099.510.0531.0987
3.374.2410010.0811.2187.3
2.943.3710010.1361.0717.1
2.672.9410010.2130.8327
2.482.6799.810.2670.8296.4
2.342.4897.810.2810.8715.6
2.222.3494.510.3140.8875.2
2.122.2289.210.3430.864.7
2.042.1284.510.3740.8913.8
1.972.0472.910.3740.9073.1
ReflectionResolution: 1.96→65.8 Å / Num. obs: 34689 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Rmerge(I) obs: 0.126 / Χ2: 0.97 / Net I/σ(I): 5.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.96-2.043.10.37426300.907172.9
2.04-2.123.80.37430800.891184.5
2.12-2.224.70.34332350.86189.2
2.22-2.345.20.31434510.887194.5
2.34-2.485.60.28135980.871197.8
2.48-2.676.40.26736420.829199.8
2.67-2.9470.21336860.8321100
2.94-3.377.10.13637171.0711100
3.37-4.247.30.08137391.2181100
4.24-5070.05339111.098199.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.1915 / WRfactor Rwork: 0.1471 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8543 / SU B: 3.718 / SU ML: 0.106 / SU R Cruickshank DPI: 0.1794 / SU Rfree: 0.1661 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2279 1734 5 %RANDOM
Rwork0.1722 ---
obs0.1751 34634 93.53 %-
all-34689 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 63.06 Å2 / Biso mean: 21.7097 Å2 / Biso min: 2.63 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20 Å20 Å2
2--0.88 Å20 Å2
3----1.42 Å2
Refinement stepCycle: LAST / Resolution: 1.96→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3648 0 146 385 4179
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0223926
X-RAY DIFFRACTIONr_angle_refined_deg1.9041.9885357
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6735464
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.32924.186172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.81415619
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9381516
X-RAY DIFFRACTIONr_chiral_restr0.1320.2563
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212986
X-RAY DIFFRACTIONr_mcbond_it1.1911.52301
X-RAY DIFFRACTIONr_mcangle_it1.94523710
X-RAY DIFFRACTIONr_scbond_it3.06831625
X-RAY DIFFRACTIONr_scangle_it4.3754.51646
LS refinement shellResolution: 1.96→2.013 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 89 -
Rwork0.243 1727 -
all-1816 -
obs--67.41 %

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