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- PDB-4tki: Crystal Structure of human Tankyrase 2 in complex with BSI-201. -

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Basic information

Entry
Database: PDB / ID: 4tki
TitleCrystal Structure of human Tankyrase 2 in complex with BSI-201.
ComponentsTankyrase-2
KeywordsTRANSFERASE / poly(ADP-ribosylation) polymerase (PARP)
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 / NAD+-protein ADP-ribosyltransferase activity / positive regulation of telomere capping / NAD+-protein poly-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 / NAD+-protein ADP-ribosyltransferase activity / positive regulation of telomere capping / NAD+-protein 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 / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Ankyrin repeat / : / Phosphoenolpyruvate Carboxykinase; domain 3 - #10 / 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. ...Ankyrin repeat / : / Phosphoenolpyruvate Carboxykinase; domain 3 - #10 / 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 / 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
4-iodo-3-nitrobenzamide / ISOPROPYL ALCOHOL / Poly [ADP-ribose] polymerase tankyrase-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.15 Å
AuthorsQiu, W. / Lam, R. / Romanov, V. / Gordon, R. / Gebremeskel, S. / Vodsedalek, J. / Thompson, C. / Beletskaya, I. / Battaile, K.P. / Pai, E.F. / Chirgadze, N.Y.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Insights into the binding of PARP inhibitors to the catalytic domain of human tankyrase-2.
Authors: Qiu, W. / Lam, R. / Voytyuk, O. / Romanov, V. / Gordon, R. / Gebremeskel, S. / Vodsedalek, J. / Thompson, C. / Beletskaya, I. / Battaile, K.P. / Pai, E.F. / Rottapel, R. / Chirgadze, N.Y.
History
DepositionMay 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 7, 2015Group: Database references
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Oct 12, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity_src_gen / pdbx_database_status / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / refine_hist / struct_keywords
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_keywords.pdbx_keywords
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)107,36722
Polymers103,9454
Non-polymers3,42218
Water9,962553
1
A: Tankyrase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0487
Polymers25,9861
Non-polymers1,0626
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tankyrase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6965
Polymers25,9861
Non-polymers7104
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Tankyrase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6965
Polymers25,9861
Non-polymers7104
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Tankyrase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9285
Polymers25,9861
Non-polymers9424
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.010, 79.470, 153.290
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Details1

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Components

#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: 25986.291 Da / Num. of mol.: 4 / Fragment: PARP, catalytic domain
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
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-33E / 4-iodo-3-nitrobenzamide / Iniparib


Mass: 292.031 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C7H5IN2O3 / Comment: inhibitor*YM
#4: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 553 / 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: 2.17 Å3/Da / Density % sol: 43.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M NaCl, 0.1M Sodium, Hepes buffer at pH7.5, 12-15% iso-propanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Aug 12, 2010 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.13→19.7 Å / Num. obs: 50089 / % possible obs: 97.9 % / Redundancy: 6.67 % / Biso Wilson estimate: 29.77 Å2 / Rmerge(I) obs: 0.124 / Net I/σ(I): 13.93 / Num. measured all: 341134
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. possibleNum. unique obsNet I/σ(I) obs% possible all
2.13-2.223.050.532314522451.3483
2.19-2.244.920.529308230182.5297.9
2.24-2.296.470.488285128503.44100
2.29-2.347.150.491261526133.7499.9
2.34-2.47.190.439283628364.24100
2.4-2.467.210.411257825784.51100
2.46-2.537.220.396270227024.75100
2.53-2.617.210.34275627565.56100
2.61-2.77.260.312270627056.13100
2.7-2.87.260.254264426447.46100
2.8-2.927.270.211268926899.37100
2.92-3.067.270.1782647264611.27100
3.06-3.237.270.1252637263715.47100
3.23-3.447.290.0942569256920.02100
3.44-3.717.230.0742518251826.11100
3.71-4.097.210.062523252332.04100
4.09-4.697.170.0472513251339.48100
4.69-5.947.120.0542534253335.24100
5.94-19.76.510.0512610251438.6296.3

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Processing

Software
NameVersionClassification
XDS2005/3data reduction
BUSTER-TNTBUSTER 2.10.0refinement
PDB_EXTRACT3.14data extraction
BUSTER2.10.0refinement
RefinementResolution: 2.15→19.39 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.9016 / SU R Cruickshank DPI: 0.226 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.243 / SU Rfree Blow DPI: 0.19 / SU Rfree Cruickshank DPI: 0.187
RfactorNum. reflection% reflectionSelection details
Rfree0.2276 1141 2.3 %RANDOM
Rwork0.1784 ---
obs0.1795 49502 99.23 %-
Displacement parametersBiso max: 119.84 Å2 / Biso mean: 29.4 Å2 / Biso min: 6.1 Å2
Baniso -1Baniso -2Baniso -3
1--4.3165 Å20 Å20 Å2
2---3.9382 Å20 Å2
3---8.2547 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: final / Resolution: 2.15→19.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6487 0 150 553 7190
Biso mean--42.86 37.26 -
Num. residues----804
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2360SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes150HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1036HARMONIC5
X-RAY DIFFRACTIONt_it6828HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion798SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7801SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6828HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg9178HARMONIC21.13
X-RAY DIFFRACTIONt_omega_torsion3.7
X-RAY DIFFRACTIONt_other_torsion17.76
LS refinement shellResolution: 2.15→2.21 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 84 2.56 %
Rwork0.2295 3200 -
all0.2302 3284 -
obs--99.23 %

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