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

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Basic information

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


negative regulation of telomeric DNA binding / negative regulation of maintenance of mitotic sister chromatid cohesion, telomeric / regulation of telomere maintenance via telomerase / XAV939 stabilizes AXIN / NAD+ ADP-ribosyltransferase / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / protein localization to chromosome, telomeric region / protein poly-ADP-ribosylation / pericentriolar material ...negative regulation of telomeric DNA binding / negative regulation of maintenance of mitotic sister chromatid cohesion, telomeric / regulation of telomere maintenance via telomerase / XAV939 stabilizes AXIN / NAD+ ADP-ribosyltransferase / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / protein localization to chromosome, telomeric region / protein poly-ADP-ribosylation / pericentriolar material / mitotic spindle pole / NAD+-protein ADP-ribosyltransferase activity / positive regulation of telomere capping / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+-protein poly-ADP-ribosyltransferase activity / mRNA transport / spindle assembly / nuclear pore / : / positive regulation of telomere maintenance via telomerase / nucleotidyltransferase activity / mitotic spindle organization / TCF dependent signaling in response to WNT / Degradation of AXIN / peptidyl-threonine phosphorylation / Wnt signaling pathway / Regulation of PTEN stability and activity / protein polyubiquitination / protein transport / positive regulation of canonical Wnt signaling pathway / histone binding / peptidyl-serine phosphorylation / nuclear membrane / chromosome, telomeric region / nuclear body / Ub-specific processing proteases / cell division / Golgi membrane / Golgi apparatus / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
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 (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
Similarity search - Domain/homology
Chem-09L / Poly [ADP-ribose] polymerase tankyrase-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 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
C: Poly [ADP-ribose] polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5699
Polymers73,0703
Non-polymers1,5006
Water9,530529
1
A: Poly [ADP-ribose] polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8563
Polymers24,3571
Non-polymers5002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Poly [ADP-ribose] polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8563
Polymers24,3571
Non-polymers5002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Poly [ADP-ribose] polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8563
Polymers24,3571
Non-polymers5002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.290, 90.410, 199.840
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Poly [ADP-ribose] polymerase / PARP


Mass: 24356.580 Da / Num. of mol.: 3
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.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-09L / 4-(3-{[4-(cyclopropylcarbonyl)piperazin-1-yl]carbonyl}-4-fluorobenzyl)phthalazin-1(2H)-one / Olaparib


Mass: 434.463 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H23FN4O3 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, inhibitor*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 529 / 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: 2.45 Å3/Da / Density % sol: 49.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: Salt: 0.4 M potassium acetate Precipitant: 22.0 %w/v PEG 4000 Buffer: 0.1 M MES (pH 6.14)

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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 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.56→57.12 Å / Num. obs: 81880 / % possible obs: 88.6 % / Redundancy: 5.9 % / CC1/2: 0.996 / Net I/σ(I): 10.2
Reflection shellResolution: 1.56→1.653 Å / Num. unique obs: 4094 / CC1/2: 0.453

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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: 1.56→57.12 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.947 / SU R Cruickshank DPI: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.105 / SU Rfree Blow DPI: 0.1 / SU Rfree Cruickshank DPI: 0.098
RfactorNum. reflection% reflectionSelection details
Rfree0.221 4031 4.92 %RANDOM
Rwork0.194 ---
obs0.195 81880 80.8 %-
Displacement parametersBiso max: 140.62 Å2 / Biso mean: 29.77 Å2 / Biso min: 11.21 Å2
Baniso -1Baniso -2Baniso -3
1--0.0159 Å20 Å20 Å2
2---0.2574 Å20 Å2
3---0.2733 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: final / Resolution: 1.56→57.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5088 0 99 529 5716
Biso mean--23.43 38.7 -
Num. residues----632
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1894SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes972HARMONIC5
X-RAY DIFFRACTIONt_it5424HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion654SEMIHARMONIC5
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_contact6531SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5424HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg7324HARMONIC21.06
X-RAY DIFFRACTIONt_omega_torsion3.71
X-RAY DIFFRACTIONt_other_torsion16.27
LS refinement shellResolution: 1.56→1.62 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.221 57 3.48 %
Rwork0.2062 1581 -
all0.2068 1638 -
obs--17 %

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