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- PDB-5fpf: Crystal structure of human tankyrase 2 in complex with TA-91 -

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Basic information

Entry
Database: PDB / ID: 5fpf
TitleCrystal structure of human tankyrase 2 in complex with TA-91
Components(TANKYRASE-2) x 2
KeywordsTRANSFERASE / PROTEIN-LIGAND COMPLEX / DIPHTHERIA TOXIN LIKE FOLD / ADP- RIBOSYLATION / TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
Function / homology
Function and homology information


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 / pericentriolar material ...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 / pericentriolar material / NAD+-protein mono-ADP-ribosyltransferase activity / NAD+ 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 / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
YefM-like fold / YefM-like fold - #10 / Ankyrin repeat / Phosphoenolpyruvate Carboxykinase; domain 3 - #10 / Other non-globular / 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) ...YefM-like fold / YefM-like fold - #10 / Ankyrin repeat / Phosphoenolpyruvate Carboxykinase; domain 3 - #10 / Other non-globular / 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 / Special / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-5ZI / Poly [ADP-ribose] polymerase tankyrase-2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHaikarainen, T. / Lehtio, L.
CitationJournal: To be Published
Title: Design, Synthesis and Evaluation of Novel Dual- Binding Inhibitors of the Tankyrases and Wnt Signalling.
Authors: Nathubhai, A. / Haikarainen, T. / Hayward, P.C. / Munoz-Descalzo, S. / Tosh, D. / Lloyd, M.D. / Lehtio, L. / Threadgill, M.D.
History
DepositionNov 30, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 2.0Sep 27, 2017Group: Atomic model / Data collection / Category: atom_site / diffrn_detector
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _diffrn_detector.type
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)55,4358
Polymers54,3774
Non-polymers1,0584
Water21612
1
B: TANKYRASE-2
D: TANKYRASE-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7174
Polymers27,1892
Non-polymers5292
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6810 Å2
ΔGint-35.3 kcal/mol
Surface area10470 Å2
MethodPISA
2
A: TANKYRASE-2
C: TANKYRASE-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7174
Polymers27,1892
Non-polymers5292
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6780 Å2
ΔGint-34.2 kcal/mol
Surface area10360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.600, 76.080, 149.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TANKYRASE-2 / TANK2 / ADP-RIBOSYLTRANSFERASE DIPHTHERIA TOXIN-LIKE 6 / ARTD 6 / POLY ADP-RIBOSE POLYMERASE 5B / ...TANK2 / ADP-RIBOSYLTRANSFERASE DIPHTHERIA TOXIN-LIKE 6 / ARTD 6 / POLY ADP-RIBOSE POLYMERASE 5B / TNKS-2 / TRF1-INTERACTING ANKYRIN - RELATED ADP-RIBOSE POLYMERASE 2 / TANKYRASE II / TANKYRASE-LIKE PROTEIN / TANKYRASE-RELATED PROTEIN


Mass: 21824.545 Da / Num. of mol.: 2 / Fragment: C-TERMINAL FRAGMENT, RESIDUES 946-1113
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): ROSETTA 2 / References: UniProt: Q9H2K2
#2: Protein/peptide TANKYRASE-2 / TANK2 / ADP-RIBOSYLTRANSFERASE DIPHTHERIA TOXIN-LIKE 6 / ARTD 6 / POLY ADP-RIBOSE POLYMERASE 5B / ...TANK2 / ADP-RIBOSYLTRANSFERASE DIPHTHERIA TOXIN-LIKE 6 / ARTD 6 / POLY ADP-RIBOSE POLYMERASE 5B / TNKS-2 / TRF1-INTERACTING ANKYRIN - RELATED ADP-RIBOSE POLYMERASE 2 / TANKYRASE II / TANKYRASE-LIKE PROTEIN / TANKYRASE-RELATED PROTEIN


Mass: 5364.037 Da / Num. of mol.: 2 / Fragment: C-TERMINAL FRAGMENT, RESIDUES 1115-1162
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): ROSETTA 2 / References: UniProt: Q9H2K2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-5ZI / 4-[3-(4-oxo-3,4-dihydroquinazolin-2- yl)propanamido]-N-(quinolin-8-yl)benzamide


Mass: 463.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H21N5O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.16 Å3/Da / Density % sol: 43 % / Description: NONE
Crystal growpH: 8.5 / Details: 0.1M BICINE PH 9.0, 16% PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.99987
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 31, 2015 / Details: MIRRORS
RadiationMonochromator: LIQUID NITROGEN COOLED CHANNEL-CUT SILICON MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 14363 / % possible obs: 94.3 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 46.71 Å2 / Rmerge(I) obs: 0.3 / Net I/σ(I): 7.2
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 1.04 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3U9Y

3u9y


Resolution: 2.6→29.415 Å / SU ML: 0.37 / σ(F): 1.35 / Phase error: 31.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2716 718 5 %
Rwork0.2134 --
obs0.2165 14325 94.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→29.415 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3300 0 72 12 3384
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093464
X-RAY DIFFRACTIONf_angle_d1.0974666
X-RAY DIFFRACTIONf_dihedral_angle_d16.5111266
X-RAY DIFFRACTIONf_chiral_restr0.04456
X-RAY DIFFRACTIONf_plane_restr0.005612
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.80070.3861440.34282722X-RAY DIFFRACTION96
2.8007-3.08220.35841390.30192651X-RAY DIFFRACTION94
3.0822-3.52760.30481450.25142743X-RAY DIFFRACTION95
3.5276-4.44190.2721420.18362698X-RAY DIFFRACTION94
4.4419-29.41710.19771480.15832793X-RAY DIFFRACTION92

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