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- PDB-5ety: Crystal Structure of human Tankyrase-1 bound to K-756 -

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Basic information

Entry
Database: PDB / ID: 5ety
TitleCrystal Structure of human Tankyrase-1 bound to K-756
ComponentsTankyrase-1
KeywordsTRANSFERASE / Tankyrase / inhibitor / non-competitive / Wnt signal
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 / protein localization to chromosome, telomeric region / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / 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 / protein localization to chromosome, telomeric region / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / protein poly-ADP-ribosylation / pericentriolar material / mitotic spindle pole / : / NAD+-protein ADP-ribosyltransferase activity / positive regulation of telomere capping / NAD+-protein poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / 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 / peptidyl-threonine phosphorylation / Degradation of AXIN / Wnt signaling pathway / Regulation of PTEN stability and activity / protein polyubiquitination / positive regulation of canonical Wnt signaling pathway / protein transport / histone binding / peptidyl-serine phosphorylation / nuclear membrane / chromosome, telomeric region / nuclear body / Ub-specific processing proteases / Golgi membrane / cell division / Golgi apparatus / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
: / 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 ...: / 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
Chem-K56 / Poly [ADP-ribose] polymerase tankyrase-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsTakahashi, Y. / Miyagi, H. / Suzuki, M. / Saito, J.
CitationJournal: Mol.Cancer Ther. / Year: 2016
Title: The Discovery and Characterization of K-756, a Novel Wnt/ beta-Catenin Pathway Inhibitor Targeting Tankyrase
Authors: Okada-Iwasaki, R. / Takahashi, Y. / Watanabe, Y. / Ishida, H. / Saito, J. / Nakai, R. / Asai, A.
History
DepositionNov 18, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Database references
Revision 1.2Feb 19, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tankyrase-1
B: Tankyrase-1
C: Tankyrase-1
D: Tankyrase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,15112
Polymers117,1564
Non-polymers1,9968
Water1,33374
1
A: Tankyrase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7883
Polymers29,2891
Non-polymers4992
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tankyrase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7883
Polymers29,2891
Non-polymers4992
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Tankyrase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7883
Polymers29,2891
Non-polymers4992
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Tankyrase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7883
Polymers29,2891
Non-polymers4992
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)158.846, 74.680, 84.603
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 1105 - 1314 / Label seq-ID: 38 - 247

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Tankyrase-1 / TANK1 / ADP-ribosyltransferase diphtheria toxin-like 5 / ARTD5 / Poly [ADP-ribose] polymerase 5A / ...TANK1 / ADP-ribosyltransferase diphtheria toxin-like 5 / ARTD5 / Poly [ADP-ribose] polymerase 5A / TNKS-1 / TRF1-interacting ankyrin-related ADP-ribose polymerase / Tankyrase I


Mass: 29288.953 Da / Num. of mol.: 4 / Fragment: UNP residues 1091-1324 / Mutation: M1266L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNKS, PARP5A, PARPL, TIN1, TINF1, TNKS1 / Production host: Escherichia coli (E. coli) / References: UniProt: O95271, 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-K56 / 3-[[1-(6,7-dimethoxyquinazolin-4-yl)piperidin-4-yl]methyl]-1,4-dihydroquinazolin-2-one


Mass: 433.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H27N5O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.14 Å3/Da / Density % sol: 42.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.8 / Details: 0.1M Na-Succinate pH 5.8, 6% PEG MME 5000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 29, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 21422 / % possible obs: 93.8 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.137 / Χ2: 1.516 / Net I/av σ(I): 12.038 / Net I/σ(I): 7.8 / Num. measured all: 84084
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.9-33.70.8719901.10489.1
3-3.123.70.43219971.1789
3.12-3.273.80.19819751.33488.7
3.27-3.443.80.13520081.35189.6
3.44-3.653.80.12520911.42791.8
3.65-3.943.90.13321311.62794.4
3.94-4.3340.13522201.87997.3
4.33-4.964.20.12323011.89499.7
4.96-6.244.20.11423121.63799.7
6.24-5040.08423971.47197.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0071refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→50 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.883 / SU B: 48.765 / SU ML: 0.411 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.539 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.3054 1098 5.2 %RANDOM
Rwork0.255 ---
obs0.2576 20069 91.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 110.29 Å2 / Biso mean: 55.05 Å2 / Biso min: 17.41 Å2
Baniso -1Baniso -2Baniso -3
1--1.38 Å2-0 Å2-0 Å2
2--0.63 Å2-0 Å2
3---0.75 Å2
Refinement stepCycle: final / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6571 0 132 74 6777
Biso mean--42.02 32.06 -
Num. residues----817
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0196880
X-RAY DIFFRACTIONr_bond_other_d0.0050.026330
X-RAY DIFFRACTIONr_angle_refined_deg1.4911.9529265
X-RAY DIFFRACTIONr_angle_other_deg1.079314506
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7675806
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.70322.978356
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.56151128
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3151553
X-RAY DIFFRACTIONr_chiral_restr0.10.2922
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027851
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021786
X-RAY DIFFRACTIONr_mcbond_it1.3082.3453257
X-RAY DIFFRACTIONr_mcbond_other1.3082.3453256
X-RAY DIFFRACTIONr_mcangle_it2.33.5114052
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A115890.07
12B115890.07
21A115190.08
22C115190.08
31A115750.09
32D115750.09
41B113790.07
42C113790.07
51B113410.08
52D113410.08
61C118000.06
62D118000.06
LS refinement shellResolution: 2.898→2.973 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.578 55 -
Rwork0.579 1132 -
all-1187 -
obs--71.29 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.5266-0.1079-0.05751.2563-0.26293.37350.00510.00070.22820.17410.02560.022-0.22820.0378-0.03080.0381-0.0249-0.00450.60480.00340.0623-36.56319.49-16.37
26.7109-0.0860.33921.47430.34723.2198-0.07730.29830.4286-0.20890.0426-0.0784-0.14-0.04670.03470.0572-0.045-0.01230.42170.0410.0782-82.75418.7-26.023
34.7939-0.5406-0.29261.41870.20692.6546-0.0588-0.2473-0.08030.08920.0204-0.07480.0564-0.17940.03840.00790.02310.00130.71860.02970.0278-81.66619.46-55.234
45.2754-0.6613-0.14851.28350.05432.6338-0.0596-0.186-0.01560.15860.013-0.0584-0.0065-0.03070.04660.0223-0.01080.00370.5694-0.02540.0559-41.796-17.12-13.001
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1105 - 1314
2X-RAY DIFFRACTION2B1105 - 1314
3X-RAY DIFFRACTION3C1105 - 1314
4X-RAY DIFFRACTION4D1105 - 1314

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