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- PDB-1xi2: Quinone Reductase 2 in Complex with Cancer Prodrug CB1954 -

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Basic information

Entry
Database: PDB / ID: 1xi2
TitleQuinone Reductase 2 in Complex with Cancer Prodrug CB1954
ComponentsNRH dehydrogenase [quinone] 2
KeywordsOXIDOREDUCTASE / QR2 / CB1954
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
5-(AZIRIDIN-1-YL)-2,4-DINITROBENZAMIDE / FLAVIN-ADENINE DINUCLEOTIDE / Ribosyldihydronicotinamide dehydrogenase [quinone]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsFu, Y. / Buryanovskyy, L. / Zhang, Z.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2005
Title: Crystal structure of quinone reductase 2 in complex with cancer prodrug CB1954
Authors: Fu, Y. / Buryanovskyy, L. / Zhang, Z.
History
DepositionSep 21, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 12, 2018Group: Data collection / Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms
Revision 1.4Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_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: NRH dehydrogenase [quinone] 2
B: NRH dehydrogenase [quinone] 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9709
Polymers51,6992
Non-polymers2,2727
Water6,521362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7980 Å2
ΔGint-25 kcal/mol
Surface area18120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.475, 106.455, 56.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


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 / Production host: Escherichia coli (E. coli)
References: UniProt: P16083, Oxidoreductases; Acting on NADH or NADPH; With unknown physiological acceptors
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / 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-CB1 / 5-(AZIRIDIN-1-YL)-2,4-DINITROBENZAMIDE / CB1954 / Tretazicar


Mass: 252.184 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H8N4O5
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 362 / 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: 2.099 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7
Details: ammonium sulfate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Apr 8, 2004
RadiationMonochromator: 1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.5→35.2 Å / Num. all: 81418 / Num. obs: 78011 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellHighest resolution: 1.5 Å / % possible all: 95.8

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→35.2 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.233 7833 random
Rwork0.216 --
all0.233 81418 -
obs0.233 78011 -
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.5→35.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3648 0 145 362 4155

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