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- PDB-3te7: Quinone Oxidoreductase (NQ02) bound to the imidazoacridin-6-one 5a1 -

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Basic information

Entry
Database: PDB / ID: 3te7
TitleQuinone Oxidoreductase (NQ02) bound to the imidazoacridin-6-one 5a1
ComponentsRibosyldihydronicotinamide dehydrogenase [quinone]
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / FAD binding protein / oxidoreductase / FAD / 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 / oxidoreductase activity / electron transfer activity / protein homodimerization activity / zinc ion binding / extracellular exosome / 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 / IMIDAZOLE / Chem-TE7 / Ribosyldihydronicotinamide dehydrogenase [quinone]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsDunstan, M.S.
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 12, 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 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_label_asym_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_label_asym_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)53,7449
Polymers51,3002
Non-polymers2,4447
Water8,413467
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7470 Å2
ΔGint-30 kcal/mol
Surface area17880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.910, 84.030, 106.550
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, 474 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-TE7 / 5-{[2-(dimethylamino)ethyl]amino}-8-methoxy-6H-imidazo[4,5,1-de]acridin-6-one


Mass: 336.388 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H20N4O2
#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.: 467 / 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: 2.48 Å3/Da / Density % sol: 50.47 %
Crystal growMethod: vapor diffusion, sitting drop / Details: VAPOR DIFFUSION, SITTING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Nov 5, 2010 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→38.9 Å / Num. all: 56473 / Num. obs: 55905 / % possible obs: 99 % / Observed criterion σ(F): 1.7 / Observed criterion σ(I): 1.7 / Redundancy: 7 % / Biso Wilson estimate: 18.41 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 16
Reflection shellResolution: 1.7→5.06 Å / % possible all: 95.4

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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
Starting model: PDB ENTRY 3FW1

3fw1


Resolution: 1.7→38.893 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8872 / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2065 2848 5.06 %random
Rwork0.1695 ---
obs0.1714 55905 98.74 %-
all-56473 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.426 Å2 / ksol: 0.343 e/Å3
Displacement parametersBiso max: 111.49 Å2 / Biso mean: 23.3359 Å2 / Biso min: 5.25 Å2
Baniso -1Baniso -2Baniso -3
1--0.0787 Å20 Å20 Å2
2---0.0172 Å2-0 Å2
3---0.0959 Å2
Refinement stepCycle: LAST / Resolution: 1.7→38.893 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3618 0 163 467 4248
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073895
X-RAY DIFFRACTIONf_angle_d1.1485311
X-RAY DIFFRACTIONf_chiral_restr0.075558
X-RAY DIFFRACTIONf_plane_restr0.005653
X-RAY DIFFRACTIONf_dihedral_angle_d20.6751436
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.72930.38491430.32922645278899
1.7293-1.76080.30851410.29442621276299
1.7608-1.79460.33951350.2732675281099
1.7946-1.83130.28591480.24532653280199
1.8313-1.87110.26761490.224526162765100
1.8711-1.91460.26091240.19792688281299
1.9146-1.96250.20331290.17892674280399
1.9625-2.01550.18381320.16462658279099
2.0155-2.07480.2161320.16482635276799
2.0748-2.14180.19381600.16852649280999
2.1418-2.21840.20281550.16552669282499
2.2184-2.30720.25151430.1632655279899
2.3072-2.41220.22861490.16022667281699
2.4122-2.53930.2051280.15427032831100
2.5393-2.69840.18441550.164126772832100
2.6984-2.90660.18831600.16326992859100
2.9066-3.1990.19551420.16722662280498
3.199-3.66160.19931420.15662690283298
3.6616-4.61210.14591380.13012733287198
4.6121-38.90290.19471430.16042726286994
Refinement TLS params.Method: refined / Origin x: 11.0608 Å / Origin y: 7.9822 Å / Origin z: 15.0847 Å
111213212223313233
T0.056 Å20.0082 Å20.007 Å2-0.0303 Å20.0015 Å2--0.0594 Å2
L0.19 °2-0.1015 °2-0.3843 °2-0.3619 °20.3123 °2--1.9336 °2
S0.0662 Å °0.0141 Å °-0.0043 Å °-0.0583 Å °0.0091 Å °-0.0367 Å °-0.2249 Å °-0.0142 Å °-0.0699 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA - B2 - 1
2X-RAY DIFFRACTION1allB - A2 - 1
3X-RAY DIFFRACTION1allA1 - 230
4X-RAY DIFFRACTION1allA - B1 - 487

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