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- PDB-4w5i: Crystal structure of human tankyrase 2 in complex with 1-methyl-7... -

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Basic information

Entry
Database: PDB / ID: 4w5i
TitleCrystal structure of human tankyrase 2 in complex with 1-methyl-7-phenyl-1,2,3,4,5,6-hexahydro-1,6- naphthyridin-5-one
ComponentsTankyrase-2
KeywordsTRANSFERASE / PROTEIN-LIGAND COMPLEX / DIPHTHERIA TOXIN LIKE FOLD / ADP- RIBOSYLATION / TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
Function / homology
Function and homology information


XAV939 stabilizes AXIN / NAD+ ADP-ribosyltransferase / protein localization to chromosome, telomeric region / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / protein poly-ADP-ribosylation / pericentriolar material / positive regulation of telomere capping / NAD+-protein ADP-ribosyltransferase activity / NAD+ ADP-ribosyltransferase activity ...XAV939 stabilizes AXIN / NAD+ ADP-ribosyltransferase / protein localization to chromosome, telomeric region / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / protein poly-ADP-ribosylation / pericentriolar material / positive regulation of telomere capping / NAD+-protein ADP-ribosyltransferase activity / NAD+ ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / positive regulation of telomere maintenance via telomerase / nucleotidyltransferase activity / TCF dependent signaling in response to WNT / Degradation of AXIN / Wnt signaling pathway / Regulation of PTEN stability and activity / protein polyubiquitination / positive regulation of canonical Wnt signaling pathway / nuclear envelope / chromosome, telomeric region / Ub-specific processing proteases / Golgi membrane / perinuclear region of cytoplasm / enzyme binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ankyrin repeat / Phosphoenolpyruvate Carboxykinase; domain 3 - #10 / Phosphoenolpyruvate Carboxykinase; domain 3 / Ankyrin repeats (many copies) / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. ...Ankyrin repeat / Phosphoenolpyruvate Carboxykinase; domain 3 - #10 / Phosphoenolpyruvate Carboxykinase; domain 3 / Ankyrin repeats (many copies) / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-3GX / Poly [ADP-ribose] polymerase tankyrase-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsHaikarainen, T. / Lehtio, L.
CitationJournal: Bioorg.Med.Chem. / Year: 2015
Title: Structure-based design, synthesis and evaluation in vitro of arylnaphthyridinones, arylpyridopyrimidinones and their tetrahydro derivatives as inhibitors of the tankyrases.
Authors: Kumpan, K. / Nathubhai, A. / Zhang, C. / Wood, P.J. / Lloyd, M.D. / Thompson, A.S. / Haikarainen, T. / Lehtio, L. / Threadgill, M.D.
History
DepositionAug 18, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tankyrase-2
B: Tankyrase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,68711
Polymers54,6002
Non-polymers1,0889
Water6,269348
1
A: Tankyrase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8906
Polymers27,3001
Non-polymers5905
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tankyrase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7985
Polymers27,3001
Non-polymers4984
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.550, 98.120, 119.220
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1316-

HOH

21A-1348-

HOH

31B-1319-

HOH

41B-1346-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Tankyrase-2 / / TANK2 / ADP-ribosyltransferase diphtheria toxin-like 6 / ARTD6 / Poly [ADP-ribose] polymerase 5B / ...TANK2 / ADP-ribosyltransferase diphtheria toxin-like 6 / ARTD6 / Poly [ADP-ribose] polymerase 5B / TNKS-2 / TRF1-interacting ankyrin-related ADP-ribose polymerase 2 / Tankyrase II / Tankyrase-like protein / Tankyrase-related protein


Mass: 27299.764 Da / Num. of mol.: 2 / Fragment: UNP residues 952-1162
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNKS2, PARP5B, TANK2, TNKL / Plasmid: PNIC28-BSA4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): ROSETTA 2 / References: UniProt: Q9H2K2, NAD+ ADP-ribosyltransferase

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Non-polymers , 5 types, 357 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-3GX / 1-methyl-7-phenyl-2,3,4,6-tetrahydro-1,6-naphthyridin-5(1H)-one


Mass: 240.300 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H16N2O
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 348 / 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: 49.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.2 M LISO4, 0.1 M TRIS HCL, 22% PEG3350, PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 9, 2013
RadiationMonochromator: single bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. all: 39384 / Num. obs: 39384 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 29.968 Å2 / Rmerge F obs: 0.996 / Rmerge(I) obs: 0.132 / Rrim(I) all: 0.144 / Rsym value: 0.144 / Χ2: 0.956 / Net I/σ(I): 9.87 / Num. measured all: 263766
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.95-26.90.7570.8642.1519901289328930.935100
2-2.060.8470.6942.6619139278327780.75199.8
2.06-2.120.8630.5663.2618691276327600.61499.9
2.12-2.180.9080.4563.9217516265526480.49699.7
2.18-2.250.910.424.2516442256725660.458100
2.25-2.330.9490.3254.9814065250324970.35899.8
2.33-2.420.9630.2726.215316240123980.29699.9
2.42-2.520.9770.2347.4516674232423240.252100
2.52-2.630.9790.28.7616011224522450.215100
2.63-2.760.9830.1799.6515019212921290.193100
2.76-2.910.9890.13712.1914476205620540.14899.9
2.91-3.080.9910.12313.8113487191419130.13399.9
3.08-3.30.9920.10515.8312411181518130.11399.9
3.3-3.560.9930.08918.0211222169316930.096100
3.56-3.90.9940.07919.9110080157515730.08799.9
3.9-4.360.9950.06821.188237141214030.07599.4
4.36-5.030.9960.06423.088035127712760.0799.9
5.03-6.170.9950.0723.787846108710860.07599.9
6.17-8.720.9960.06624.2159868468460.071100
8.720.9970.05725.9832125074890.06296.4

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Processing

Software
NameVersionClassification
XDSdata reduction
REFMAC5.7.0029refinement
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→29.18 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.148 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.133 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1999 1970 5 %RANDOM
Rwork0.162 37413 --
obs0.1639 37413 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 82.28 Å2 / Biso mean: 27.67 Å2 / Biso min: 14.12 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å20 Å20 Å2
2---1.16 Å2-0 Å2
3---1.69 Å2
Refinement stepCycle: final / Resolution: 1.95→29.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3346 0 64 352 3762
Biso mean--26.68 36.45 -
Num. residues----417
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193537
X-RAY DIFFRACTIONr_bond_other_d0.0010.023261
X-RAY DIFFRACTIONr_angle_refined_deg1.4091.954775
X-RAY DIFFRACTIONr_angle_other_deg0.7793.0027488
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0265427
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.73622.857182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.10615586
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.441529
X-RAY DIFFRACTIONr_chiral_restr0.0860.2478
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024060
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02921
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 144 -
Rwork0.263 2733 -
all-2877 -
obs--99.97 %

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