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

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Basic information

Entry
Database: PDB / ID: 7kkq
TitleStructure of the catalytic domain of tankyrase 1 in complex with veliparib
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 / protein auto-ADP-ribosylation / protein localization to chromosome, telomeric region / negative regulation of telomere maintenance via telomere lengthening ...: / 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 / 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 / mitotic spindle pole / NAD+-protein mono-ADP-ribosyltransferase activity / pericentriolar material / Transferases; Glycosyltransferases; Pentosyltransferases / peptidyl-threonine phosphorylation / NAD+ poly-ADP-ribosyltransferase activity / 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 / Regulation of PTEN stability and activity / Wnt signaling pathway / 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 / cytosol / cytoplasm
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-78P / Poly [ADP-ribose] polymerase tankyrase-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)98,66512
Polymers97,4264
Non-polymers1,2398
Water15,006833
1
A: Poly [ADP-ribose] polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6663
Polymers24,3571
Non-polymers3102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Poly [ADP-ribose] polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6663
Polymers24,3571
Non-polymers3102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Poly [ADP-ribose] polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6663
Polymers24,3571
Non-polymers3102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Poly [ADP-ribose] polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6663
Polymers24,3571
Non-polymers3102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.190, 159.100, 84.270
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 24356.580 Da / Num. of mol.: 4
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-78P / (2R)-2-(7-carbamoyl-1H-benzimidazol-2-yl)-2-methylpyrrolidinium / Veliparib


Mass: 244.292 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H16N4O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 833 / 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: 2.62 Å3/Da / Density % sol: 53.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: Buffer: 0.1 M Sodium Citrate (pH 5.60) Salt: 1.0 M ammonium formate Precipitant: 23.0 %w/v PEG 4000

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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: Dec 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.59→79.55 Å / Num. obs: 110379 / % possible obs: 92.8 % / Redundancy: 6.4 % / CC1/2: 0.999 / Net I/σ(I): 19.1
Reflection shellResolution: 1.59→1.7 Å / Num. unique obs: 5514 / CC1/2: 0.786

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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: 1.59→79.55 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / SU R Cruickshank DPI: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.116 / SU Rfree Blow DPI: 0.108 / SU Rfree Cruickshank DPI: 0.104
RfactorNum. reflection% reflectionSelection details
Rfree0.23 5532 5.01 %RANDOM
Rwork0.204 ---
obs0.205 110379 79.5 %-
Displacement parametersBiso max: 112.37 Å2 / Biso mean: 30.17 Å2 / Biso min: 13.85 Å2
Baniso -1Baniso -2Baniso -3
1-0.0892 Å20 Å20 Å2
2---0.1857 Å20 Å2
3---0.0965 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: final / Resolution: 1.59→79.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6651 0 76 833 7560
Biso mean--22.84 42.08 -
Num. residues----824
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2482SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1234HARMONIC5
X-RAY DIFFRACTIONt_it7040HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion861SEMIHARMONIC5
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_contact8408SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7040HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg9494HARMONIC21.05
X-RAY DIFFRACTIONt_omega_torsion3.98
X-RAY DIFFRACTIONt_other_torsion15.51
LS refinement shellResolution: 1.59→1.65 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.197 106 4.8 %
Rwork0.2199 2102 -
all0.2188 2208 -
obs--15.1 %

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