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- PDB-7kkp: Structure of the catalytic domain of tankyrase 1 in complex with ... -

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Basic information

Entry
Database: PDB / ID: 7kkp
TitleStructure of the catalytic domain of tankyrase 1 in complex with niraparib
ComponentsPoly [ADP-ribose] polymerase
KeywordsTRANSFERASE / PARP1
Function / homology
Function and homology information


: / negative regulation of maintenance of mitotic sister chromatid cohesion, telomeric / positive regulation of telomere maintenance via telomere lengthening / regulation of telomere maintenance via telomerase / 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 ...: / negative regulation of maintenance of mitotic sister chromatid cohesion, telomeric / positive regulation of telomere maintenance via telomere lengthening / regulation of telomere maintenance via telomerase / 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 / mitotic spindle pole / NAD+-protein mono-ADP-ribosyltransferase activity / pericentriolar material / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ poly-ADP-ribosyltransferase activity / peptidyl-threonine phosphorylation / mRNA transport / nuclear pore / spindle assembly / positive regulation of telomere maintenance via telomerase / nucleotidyltransferase activity / mitotic spindle organization / TCF dependent signaling in response to WNT / Degradation of AXIN / peptidyl-serine phosphorylation / Wnt signaling pathway / Regulation of PTEN stability and activity / protein polyubiquitination / positive regulation of canonical Wnt signaling pathway / protein transport / nuclear membrane / histone binding / chromosome, telomeric region / Ub-specific processing proteases / nuclear body / Golgi membrane / cell division / Golgi apparatus / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
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) ...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-3JD / Poly [ADP-ribose] polymerase tankyrase-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsGajiwala, K.S. / Ryan, K.
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Dissecting the molecular determinants of clinical PARP1 inhibitor selectivity for tankyrase1.
Authors: Ryan, K. / Bolanos, B. / Smith, M. / Palde, P.B. / Cuenca, P.D. / VanArsdale, T.L. / Niessen, S. / Zhang, L. / Behenna, D. / Ornelas, M.A. / Tran, K.T. / Kaiser, S. / Lum, L. / Stewart, A. / Gajiwala, K.S.
History
DepositionOct 27, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 6, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Apr 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Poly [ADP-ribose] polymerase
B: Poly [ADP-ribose] polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,15713
Polymers48,7132
Non-polymers1,44411
Water9,728540
1
A: Poly [ADP-ribose] polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0316
Polymers24,3571
Non-polymers6745
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Poly [ADP-ribose] polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1277
Polymers24,3571
Non-polymers7706
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.370, 74.080, 151.760
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 / PARP


Mass: 24356.580 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
References: UniProt: Q59FX0, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-3JD / 2-{4-[(3S)-piperidin-3-yl]phenyl}-2H-indazole-7-carboxamide / Niraparib


Mass: 320.388 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H20N4O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 540 / 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: 2.5 Å3/Da / Density % sol: 50.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: Buffer: 0.1 M Sodium acetate trihydrate (pH 5.50) Salt: 0.2 M lithium sulfate monohydrate Precipitant: 30.0 %v/v iso-propanol Precipitant: 10.0 %w/v PEG 1500

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Data collection

DiffractionMean temperature: 98 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→75.88 Å / Num. obs: 75846 / % possible obs: 92.7 % / Redundancy: 6.1 % / CC1/2: 0.999 / Net I/σ(I): 15.6
Reflection shellResolution: 1.42→1.51 Å / Num. unique obs: 3785 / CC1/2: 0.538

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
PDB_EXTRACT3.25data extraction
Aimlessdata scaling
PHASERphasing
autoPROCdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2rf5

2rf5


Resolution: 1.4→41.78 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.947 / SU R Cruickshank DPI: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.079 / SU Rfree Blow DPI: 0.077 / SU Rfree Cruickshank DPI: 0.072
RfactorNum. reflection% reflectionSelection details
Rfree0.208 3700 4.88 %RANDOM
Rwork0.187 ---
obs0.188 75846 78.4 %-
Displacement parametersBiso max: 159.35 Å2 / Biso mean: 20.89 Å2 / Biso min: 7.38 Å2
Baniso -1Baniso -2Baniso -3
1-0.0221 Å20 Å20 Å2
2---0.1271 Å20 Å2
3---0.1051 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: final / Resolution: 1.4→41.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3332 0 79 540 3951
Biso mean--32.09 32.38 -
Num. residues----412
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1241SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes628HARMONIC5
X-RAY DIFFRACTIONt_it3562HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion430SEMIHARMONIC5
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_contact4343SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3562HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4807HARMONIC21.01
X-RAY DIFFRACTIONt_omega_torsion4.35
X-RAY DIFFRACTIONt_other_torsion14.7
LS refinement shellResolution: 1.4→1.47 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2376 74 4.88 %
Rwork0.2195 1443 -
all0.2205 1517 -
obs--12.12 %

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