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- PDB-7o6x: Tankyrase 2 in complex with an inhibitor (OM-153) -

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Basic information

Entry
Database: PDB / ID: 7o6x
TitleTankyrase 2 in complex with an inhibitor (OM-153)
Components(Poly [ADP-ribose] polymerase tankyrase-2) x 2
KeywordsTRANSFERASE / Inhibitor / Complex / Poly-ADP-ribosylation / Enzyme
Function / homology
Function and homology information


XAV939 stabilizes AXIN / positive regulation of telomere capping / NAD+ ADP-ribosyltransferase / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / protein localization to chromosome, telomeric region / NAD+-protein-aspartate ADP-ribosyltransferase activity / protein poly-ADP-ribosylation / NAD+-protein-glutamate ADP-ribosyltransferase activity / pericentriolar material ...XAV939 stabilizes AXIN / positive regulation of telomere capping / NAD+ ADP-ribosyltransferase / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / protein localization to chromosome, telomeric region / NAD+-protein-aspartate ADP-ribosyltransferase activity / protein poly-ADP-ribosylation / NAD+-protein-glutamate ADP-ribosyltransferase activity / pericentriolar material / NAD+-protein mono-ADP-ribosyltransferase activity / NAD+ poly-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 / 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 repeat / 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
Similarity search - Domain/homology
Chem-V4Q / Poly [ADP-ribose] polymerase tankyrase-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSowa, S.T. / Lehtio, L.
Funding support Finland, 2items
OrganizationGrant numberCountry
Academy of Finland287063, 294085 Finland
Jane and Aatos Erkko Foundation Finland
CitationJournal: J.Med.Chem. / Year: 2021
Title: Development of a 1,2,4-Triazole-Based Lead Tankyrase Inhibitor: Part II.
Authors: Leenders, R.G.G. / Brinch, S.A. / Sowa, S.T. / Amundsen-Isaksen, E. / Galera-Prat, A. / Murthy, S. / Aertssen, S. / Smits, J.N. / Nieczypor, P. / Damen, E. / Wegert, A. / Nazare, M. / ...Authors: Leenders, R.G.G. / Brinch, S.A. / Sowa, S.T. / Amundsen-Isaksen, E. / Galera-Prat, A. / Murthy, S. / Aertssen, S. / Smits, J.N. / Nieczypor, P. / Damen, E. / Wegert, A. / Nazare, M. / Lehtio, L. / Waaler, J. / Krauss, S.
History
DepositionApr 12, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 2.0Mar 16, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_asym / struct_conf / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _entity_poly_seq.entity_id / _entity_poly_seq.num / _pdbx_entity_nonpoly.entity_id / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_poly_seq_scheme.asym_id / _pdbx_poly_seq_scheme.entity_id / _pdbx_poly_seq_scheme.ndb_seq_num / _pdbx_poly_seq_scheme.pdb_strand_id / _pdbx_poly_seq_scheme.seq_id / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_sheet_hbond.range_1_auth_asym_id / _pdbx_struct_sheet_hbond.range_1_label_asym_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_asym_id / _pdbx_struct_sheet_hbond.range_2_label_asym_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_residues.auth_asym_id / _pdbx_unobs_or_zero_occ_residues.label_asym_id / _pdbx_unobs_or_zero_occ_residues.label_seq_id / _struct_conf.beg_auth_asym_id / _struct_conf.beg_label_asym_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_asym_id / _struct_conf.end_label_asym_id / _struct_conf.end_label_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.align_id / _struct_sheet_range.beg_auth_asym_id / _struct_sheet_range.beg_label_asym_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_asym_id / _struct_sheet_range.end_label_asym_id / _struct_sheet_range.end_label_seq_id
Revision 2.1Aug 2, 2023Group: Database references / Derived calculations / Category: atom_type / citation / citation_author
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
BBB: Poly [ADP-ribose] polymerase tankyrase-2
A: Poly [ADP-ribose] polymerase tankyrase-2
AAA: Poly [ADP-ribose] polymerase tankyrase-2
B: Poly [ADP-ribose] polymerase tankyrase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8428
Polymers49,6924
Non-polymers1,1504
Water2,234124
1
BBB: Poly [ADP-ribose] polymerase tankyrase-2
B: Poly [ADP-ribose] polymerase tankyrase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4214
Polymers24,8462
Non-polymers5752
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Poly [ADP-ribose] polymerase tankyrase-2
AAA: Poly [ADP-ribose] polymerase tankyrase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4214
Polymers24,8462
Non-polymers5752
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.390, 76.430, 147.730
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 19482.053 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNKS2, PARP5B, TANK2, TNKL / Production host: Escherichia coli (E. coli)
References: UniProt: Q9H2K2, NAD+ ADP-ribosyltransferase, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Protein/peptide Poly [ADP-ribose] polymerase tankyrase-2 / ADP-ribosyltransferase diphtheria toxin-like 6 / ARTD6 / Poly [ADP-ribose] polymerase 5B / Protein ...ADP-ribosyltransferase diphtheria toxin-like 6 / ARTD6 / Poly [ADP-ribose] polymerase 5B / Protein poly-ADP-ribosyltransferase tankyrase-2 / TNKS-2 / TRF1-interacting ankyrin-related ADP-ribose polymerase 2 / Tankyrase II / Tankyrase-2 / TANK2 / Tankyrase-like protein / Tankyrase-related protein


Mass: 5364.037 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNKS2, PARP5B, TANK2, TNKL / Production host: Escherichia coli (E. coli)
References: UniProt: Q9H2K2, NAD+ ADP-ribosyltransferase, Transferases; Glycosyltransferases; Pentosyltransferases
#3: Chemical ChemComp-V4Q / N-[3-[5-(5-ethoxypyridin-2-yl)-4-(2-fluorophenyl)-1,2,4-triazol-3-yl]cyclobutyl]quinoxaline-5-carboxamide / 146282356


Mass: 509.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H24FN7O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.35 Å3/Da / Density % sol: 47.72 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / Details: 22.5% PEG6000, Bicine pH=8.75

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 24609 / % possible obs: 100 % / Redundancy: 13.36 % / CC1/2: 0.996 / Net I/σ(I): 7.53
Reflection shellResolution: 2.2→2.26 Å / Num. unique obs: 1785 / CC1/2: 0.841

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NOB

5nob


Resolution: 2.2→41.43 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.924 / WRfactor Rfree: 0.241 / WRfactor Rwork: 0.196 / SU B: 8.079 / SU ML: 0.192 / Average fsc free: 0.8634 / Average fsc work: 0.8787 / Cross valid method: FREE R-VALUE / ESU R: 0.282 / ESU R Free: 0.222
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2582 1231 5.002 %
Rwork0.2112 23378 -
all0.214 --
obs-24609 99.963 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 38.595 Å2
Baniso -1Baniso -2Baniso -3
1-3.483 Å20 Å20 Å2
2--0.563 Å2-0 Å2
3----4.047 Å2
Refinement stepCycle: LAST / Resolution: 2.2→41.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3217 0 78 124 3419
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0133405
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173053
X-RAY DIFFRACTIONr_angle_refined_deg1.1971.6494586
X-RAY DIFFRACTIONr_angle_other_deg1.0781.5827018
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7085398
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3120.865208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.19315557
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9781529
X-RAY DIFFRACTIONr_chiral_restr0.040.2407
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023904
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02872
X-RAY DIFFRACTIONr_nbd_refined0.1620.2582
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1620.22814
X-RAY DIFFRACTIONr_nbtor_refined0.160.21544
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0680.21550
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2155
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1480.213
X-RAY DIFFRACTIONr_nbd_other0.1380.244
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1210.211
X-RAY DIFFRACTIONr_mcbond_it1.54.0561604
X-RAY DIFFRACTIONr_mcbond_other1.54.0551603
X-RAY DIFFRACTIONr_mcangle_it2.6046.0661998
X-RAY DIFFRACTIONr_mcangle_other2.6036.0681999
X-RAY DIFFRACTIONr_scbond_it1.4994.1771801
X-RAY DIFFRACTIONr_scbond_other1.4984.1771802
X-RAY DIFFRACTIONr_scangle_it2.5796.1852584
X-RAY DIFFRACTIONr_scangle_other2.5786.1852585
X-RAY DIFFRACTIONr_lrange_it4.33644.9853697
X-RAY DIFFRACTIONr_lrange_other4.31744.9553689
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2570.282890.3151693X-RAY DIFFRACTION99.9439
2.257-2.3190.404880.2951661X-RAY DIFFRACTION99.9429
2.319-2.3860.31840.2791596X-RAY DIFFRACTION100
2.386-2.460.264820.271574X-RAY DIFFRACTION99.9397
2.46-2.540.306790.251501X-RAY DIFFRACTION100
2.54-2.6290.251790.2421485X-RAY DIFFRACTION100
2.629-2.7290.274750.2251435X-RAY DIFFRACTION100
2.729-2.840.264710.221352X-RAY DIFFRACTION99.9298
2.84-2.9660.295710.2081350X-RAY DIFFRACTION100
2.966-3.1110.255660.2021239X-RAY DIFFRACTION100
3.111-3.2790.256630.1941200X-RAY DIFFRACTION100
3.279-3.4780.251610.1981167X-RAY DIFFRACTION100
3.478-3.7180.286560.1891066X-RAY DIFFRACTION99.9109
3.718-4.0160.25540.1891015X-RAY DIFFRACTION100
4.016-4.3990.236490.169935X-RAY DIFFRACTION100
4.399-4.9170.176450.17851X-RAY DIFFRACTION100
4.917-5.6770.248400.198764X-RAY DIFFRACTION100
5.677-6.950.364350.231668X-RAY DIFFRACTION100
6.95-9.8180.17270.199514X-RAY DIFFRACTION100

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