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- PDB-5lbz: Structure of the human quinone reductase 2 (NQO2) in complex with... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5lbz | ||||||
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Title | Structure of the human quinone reductase 2 (NQO2) in complex with pacritinib | ||||||
![]() | Ribosyldihydronicotinamide dehydrogenase [quinone] | ||||||
![]() | OXIDOREDUCTASE / quinone reductase 2 / kinase inhibitor / pancritinib / Ribosyldihydronicotinamide dehydrogenase (NQO2) | ||||||
Function / homology | ![]() 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 | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Schneider, S. / Medard, G. / Kuster, B. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The target landscape of clinical kinase drugs. Authors: Klaeger, S. / Heinzlmeir, S. / Wilhelm, M. / Polzer, H. / Vick, B. / Koenig, P.A. / Reinecke, M. / Ruprecht, B. / Petzoldt, S. / Meng, C. / Zecha, J. / Reiter, K. / Qiao, H. / Helm, D. / ...Authors: Klaeger, S. / Heinzlmeir, S. / Wilhelm, M. / Polzer, H. / Vick, B. / Koenig, P.A. / Reinecke, M. / Ruprecht, B. / Petzoldt, S. / Meng, C. / Zecha, J. / Reiter, K. / Qiao, H. / Helm, D. / Koch, H. / Schoof, M. / Canevari, G. / Casale, E. / Depaolini, S.R. / Feuchtinger, A. / Wu, Z. / Schmidt, T. / Rueckert, L. / Becker, W. / Huenges, J. / Garz, A.K. / Gohlke, B.O. / Zolg, D.P. / Kayser, G. / Vooder, T. / Preissner, R. / Hahne, H. / Tonisson, N. / Kramer, K. / Gotze, K. / Bassermann, F. / Schlegl, J. / Ehrlich, H.C. / Aiche, S. / Walch, A. / Greif, P.A. / Schneider, S. / Felder, E.R. / Ruland, J. / Medard, G. / Jeremias, I. / Spiekermann, K. / Kuster, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 225.6 KB | Display | ![]() |
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PDB format | ![]() | 177.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5lbwC ![]() 5lbyC ![]() 5m5aC ![]() 5mafC ![]() 5magC ![]() 5mahC ![]() 5maiC ![]() 5lbuS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 3 - 229 / Label seq-ID: 4 - 230
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 26775.398 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P16083, ribosyldihydronicotinamide dehydrogenase (quinone) |
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-Non-polymers , 5 types, 437 molecules ![](data/chem/img/FAD.gif)
![](data/chem/img/6T3.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/6T3.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 49.06 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: 200 mM sodium sulphate, 2.2 M ammonium sulphate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 30, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→48.6 Å / Num. obs: 97699 / % possible obs: 95 % / Redundancy: 4.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Net I/σ(I): 21.11 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.329 / Mean I/σ(I) obs: 5.3 / % possible all: 91 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5LBU Resolution: 1.4→48.6 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.146 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.044 / ESU R Free: 0.041 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.062 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→48.6 Å
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Refine LS restraints |
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