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- PDB-3tem: Quinone Oxidoreductase (NQ02) bound to the imidazoacridin-6-one 6a1 -

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Basic information

Entry
Database: PDB / ID: 3tem
TitleQuinone Oxidoreductase (NQ02) bound to the imidazoacridin-6-one 6a1
ComponentsRibosyldihydronicotinamide dehydrogenase [quinone]
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / 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
Chem-6A1 / FLAVIN-ADENINE DINUCLEOTIDE / IMIDAZOLE / Ribosyldihydronicotinamide dehydrogenase [quinone]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsDunstan, M.S. / Leys, D.
CitationJournal: J.Med.Chem. / Year: 2011
Title: Novel Inhibitors of NRH:Quinone Oxidoreductase 2 (NQO2): Crystal Structures, Biochemical Activity, and Intracellular Effects of Imidazoacridin-6-ones.
Authors: Dunstan, M.S. / Barnes, J. / Humphries, M. / Whitehead, R.C. / Bryce, R.A. / Leys, D. / Stratford, I.J. / Nolan, K.A.
History
DepositionAug 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2011Group: Database references
Revision 1.2Oct 19, 2011Group: Database references
Revision 1.3Feb 28, 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_ref_seq_dif / 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_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_label_asym_id / _struct_ref_seq_dif.details / _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)53,7869
Polymers51,3002
Non-polymers2,4867
Water8,593477
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7510 Å2
ΔGint-30 kcal/mol
Surface area17810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.764, 83.571, 106.281
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 25650.129 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) / References: UniProt: P16083, EC: 1.10.99.2

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Non-polymers , 5 types, 484 molecules

#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-6A1 / hydroxy(2-{[(5S)-6-hydroxy-8-methoxy-4,5-dihydro-3H-imidazo[4,5,1-de]acridin-5-yl]amino}ethyl)dimethylammonium


Mass: 357.427 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H25N4O3
#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 477 / 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: 2.46 Å3/Da / Density % sol: 49.94 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: May 11, 2010
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→28.29 Å / Num. all: 90301 / Num. obs: 88590 / % possible obs: 99.4 % / Observed criterion σ(F): 1.49 / Observed criterion σ(I): 1.49 / Biso Wilson estimate: 14.37 Å2

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Processing

Software
NameVersionClassificationNB
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→28.281 Å / Occupancy max: 1 / Occupancy min: 0.88 / FOM work R set: 0.9097 / SU ML: 0.14 / σ(F): 1.34 / Phase error: 15.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1651 4449 5.02 %
Rwork0.1491 --
obs0.1499 88576 98.2 %
Solvent computationShrinkage radii: 0.65 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.982 Å2 / ksol: 0.433 e/Å3
Displacement parametersBiso max: 120.78 Å2 / Biso mean: 24.4693 Å2 / Biso min: 6.57 Å2
Baniso -1Baniso -2Baniso -3
1-0.5763 Å20 Å2-0 Å2
2---0.2348 Å20 Å2
3----0.3415 Å2
Refinement stepCycle: LAST / Resolution: 1.45→28.281 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3618 0 165 477 4260
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123897
X-RAY DIFFRACTIONf_angle_d1.4925317
X-RAY DIFFRACTIONf_chiral_restr0.08556
X-RAY DIFFRACTIONf_plane_restr0.008653
X-RAY DIFFRACTIONf_dihedral_angle_d21.491450
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.45-1.46650.26751170.28562318243582
1.4665-1.48370.29481540.25432432258687
1.4837-1.50180.24981580.24852524268291
1.5018-1.52080.26691310.23972668279994
1.5208-1.54080.2271220.22072735285797
1.5408-1.5620.2541340.202528432977100
1.562-1.58430.21061620.191328162978100
1.5843-1.60790.20381330.172328592992100
1.6079-1.6330.21481620.176928092971100
1.633-1.65980.19321180.160128362954100
1.6598-1.68840.18791560.160428172973100
1.6884-1.71910.16731650.154528353000100
1.7191-1.75220.17831220.152428152937100
1.7522-1.78790.19171580.152628543012100
1.7879-1.82680.17521340.149328693003100
1.8268-1.86930.17161590.14928002959100
1.8693-1.9160.17241560.147328402996100
1.916-1.96780.1671190.143528802999100
1.9678-2.02570.17131620.137928362998100
2.0257-2.09110.1451460.146428522998100
2.0911-2.16580.16991810.145328142995100
2.1658-2.25250.14721630.134928613024100
2.2525-2.35490.14321570.127928623019100
2.3549-2.4790.15861580.128328603018100
2.479-2.63420.12921530.132528583011100
2.6342-2.83750.151710.141228793050100
2.8375-3.12270.14011390.146428993038100
3.1227-3.57380.1811590.144929173076100
3.5738-4.49960.13831440.126929443088100
4.4996-28.28620.14771560.152995315197
Refinement TLS params.Method: refined / Origin x: -11.0071 Å / Origin y: -7.9819 Å / Origin z: 15.1301 Å
111213212223313233
T0.074 Å20.0131 Å2-0.0088 Å2-0.0498 Å2-0.003 Å2--0.0875 Å2
L0.2648 °2-0.0536 °20.3521 °2-0.349 °2-0.2738 °2--2.0178 °2
S0.0571 Å °0.0125 Å °-0.0068 Å °-0.0523 Å °0.013 Å °0.0303 Å °0.2224 Å °0.0182 Å °-0.0654 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 229
2X-RAY DIFFRACTION1allA - B231 - 501
3X-RAY DIFFRACTION1allB2 - 229
4X-RAY DIFFRACTION1allB - A231 - 501
5X-RAY DIFFRACTION1allB1 - 541
6X-RAY DIFFRACTION1allA1

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