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- PDB-5adq: Crystal structure of human tankyrase 2 in complex with JW55 -

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Basic information

Entry
Database: PDB / ID: 5adq
TitleCrystal structure of human tankyrase 2 in complex with JW55
Components(TANKYRASE-2) x 2
KeywordsTRANSFERASE / PROTEIN-LIGAND COMPLEX / DIPHTHERIA TOXIN LIKE FOLD / ADP- RIBOSYLATION / TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
Function / homology
Function and homology information


XAV939 stabilizes AXIN / positive regulation of telomere capping / NAD+ ADP-ribosyltransferase / protein auto-ADP-ribosylation / protein localization to chromosome, telomeric region / negative regulation of telomere maintenance via telomere lengthening / NAD+-protein-aspartate ADP-ribosyltransferase activity / protein poly-ADP-ribosylation / NAD+-protein-glutamate ADP-ribosyltransferase activity / NAD+-protein mono-ADP-ribosyltransferase activity ...XAV939 stabilizes AXIN / positive regulation of telomere capping / NAD+ ADP-ribosyltransferase / protein auto-ADP-ribosylation / protein localization to chromosome, telomeric region / negative regulation of telomere maintenance via telomere lengthening / NAD+-protein-aspartate ADP-ribosyltransferase activity / protein poly-ADP-ribosylation / NAD+-protein-glutamate ADP-ribosyltransferase activity / NAD+-protein mono-ADP-ribosyltransferase activity / pericentriolar material / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ poly-ADP-ribosyltransferase activity / positive regulation of telomere maintenance via telomerase / nucleotidyltransferase activity / TCF dependent signaling in response to WNT / Degradation of AXIN / Regulation of PTEN stability and activity / Wnt signaling pathway / protein polyubiquitination / nuclear envelope / positive regulation of canonical Wnt signaling pathway / chromosome, telomeric region / Ub-specific processing proteases / Golgi membrane / perinuclear region of cytoplasm / enzyme binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
YefM-like fold / YefM-like fold - #10 / Ankyrin repeat / Phosphoenolpyruvate Carboxykinase; domain 3 - #10 / Other non-globular / Phosphoenolpyruvate Carboxykinase; domain 3 / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / SAM domain (Sterile alpha motif) ...YefM-like fold / YefM-like fold - #10 / Ankyrin repeat / Phosphoenolpyruvate Carboxykinase; domain 3 - #10 / Other non-globular / Phosphoenolpyruvate Carboxykinase; domain 3 / 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 / Special / 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-A95 / BICARBONATE ION / Poly [ADP-ribose] polymerase tankyrase-2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHaikarainen, T. / Lehtio, L.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2016
Title: Development and Structural Analysis of Adenosine Site Binding Tankyrase Inhibitors.
Authors: Haikarainen, T. / Waaler, J. / Ignatev, A. / Nkizinkiko, Y. / Venkannagari, H. / Obaji, E. / Krauss, S. / Lehtio, L.
History
DepositionAug 24, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: TANKYRASE-2
B: TANKYRASE-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0348
Polymers27,1892
Non-polymers8456
Water1,76598
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6790 Å2
ΔGint-64.2 kcal/mol
Surface area10540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.170, 66.170, 121.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-2060-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein TANKYRASE-2 / TANK2 / ADP-RIBOSYLTRANSFERASE DIPHTHERIA TOXIN-LIKE 6 / ARTD 6 / POLY ADP-RIBOSE POLYMERASE 5B / ...TANK2 / ADP-RIBOSYLTRANSFERASE DIPHTHERIA TOXIN-LIKE 6 / ARTD 6 / POLY ADP-RIBOSE POLYMERASE 5B / TNKS-2 / TRF1-INTERACTING ANKYRIN - RELATED ADP-RIBOSE POLYMERASE 2 / TANKYRASE II / TANKYRASE-LIKE PROTEIN / TANKYRASE-RELATED PROTEIN


Mass: 21824.545 Da / Num. of mol.: 1 / Fragment: C-TERMINAL FRAGMENT, RESIDUES 946-1113
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): ROSETTA 2 / References: UniProt: Q9H2K2
#2: Protein/peptide TANKYRASE-2 / TANK2 / ADP-RIBOSYLTRANSFERASE DIPHTHERIA TOXIN-LIKE 6 / ARTD 6 / POLY ADP-RIBOSE POLYMERASE 5B / ...TANK2 / ADP-RIBOSYLTRANSFERASE DIPHTHERIA TOXIN-LIKE 6 / ARTD 6 / POLY ADP-RIBOSE POLYMERASE 5B / TNKS-2 / TRF1-INTERACTING ANKYRIN - RELATED ADP-RIBOSE POLYMERASE 2 / TANKYRASE II / TANKYRASE-LIKE PROTEIN / TANKYRASE-RELATED PROTEIN


Mass: 5364.037 Da / Num. of mol.: 1 / Fragment: C-TERMINAL FRAGMENT, RESIDUES 1115-1162
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): ROSETTA 2 / References: UniProt: Q9H2K2

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Non-polymers , 6 types, 104 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-A95 / N-(4-(((4-(4-methoxyphenyl)oxan-4- yl)methyl)carbamoyl)phenyl)furan-2-carboxamide / JW55 Inhibitor


Mass: 434.484 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H26N2O5
#6: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.4 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growpH: 8.5 / Details: 0.2 M LISO4, 0.1 M TRIS HCL, 22 % PEG 3350, PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 29, 2012 / Details: MIRRORS
RadiationMonochromator: DIAMOND (001) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 16426 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.4
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 7 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KR7

3kr7


Resolution: 2.1→46.79 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.921 / SU B: 4.189 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23784 822 5 %RANDOM
Rwork0.18797 ---
obs0.19044 15603 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.04 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2---0.1 Å20 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 2.1→46.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1670 0 53 98 1821
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191768
X-RAY DIFFRACTIONr_bond_other_d0.0020.021225
X-RAY DIFFRACTIONr_angle_refined_deg1.4841.962381
X-RAY DIFFRACTIONr_angle_other_deg0.88132945
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4925208
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.79222.88990
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.59615287
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6881514
X-RAY DIFFRACTIONr_chiral_restr0.0870.2236
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021985
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02401
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 51 -
Rwork0.234 999 -
obs--100 %

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