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- PDB-5fpg: Crystal structure of human tankyrase 2 in complex with TA-92 -

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Basic information

Entry
Database: PDB / ID: 5fpg
TitleCrystal structure of human tankyrase 2 in complex with TA-92
ComponentsTANKYRASE-2
KeywordsTRANSFERASE / PROTEIN-LIGAND COMPLEX / DIPHTHERIA TOXIN LIKE FOLD / ADP- RIBOSYLATION / TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
Function / homology
Function and homology information


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 / positive regulation of telomere capping / NAD+-protein ADP-ribosyltransferase activity / NAD+-protein poly-ADP-ribosyltransferase activity ...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 / positive regulation of telomere capping / NAD+-protein ADP-ribosyltransferase activity / NAD+-protein 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 / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
: / Ankyrin repeat / Phosphoenolpyruvate Carboxykinase; domain 3 - #10 / Phosphoenolpyruvate Carboxykinase; domain 3 / 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. ...: / Ankyrin repeat / Phosphoenolpyruvate Carboxykinase; domain 3 - #10 / Phosphoenolpyruvate Carboxykinase; domain 3 / 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-Q28 / Poly [ADP-ribose] polymerase tankyrase-2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.75 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 1.1Sep 13, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 2.0Oct 23, 2019Group: Atomic model / Data collection / Other / Category: atom_site / pdbx_database_status
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 / _pdbx_database_status.status_code_sf
Revision 2.1May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6856
Polymers54,6002
Non-polymers1,0864
Water45025
1
A: TANKYRASE-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8433
Polymers27,3001
Non-polymers5432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TANKYRASE-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8433
Polymers27,3001
Non-polymers5432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.990, 76.560, 148.830
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: 27299.764 Da / Num. of mol.: 2 / Fragment: C-TERMINAL FRAGMENT, UNP RESIDUES 946-1162
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
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-Q28 / 4-[3-(8-METHYL-4-OXO-3,4-DIHYDROQUINAZOLIN-2- YL)PROPANAMIDO]-N-(QUINOLIN-8-YL)BENZAMIDE


Mass: 477.514 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H23N5O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.2 Å3/Da / Density % sol: 44 % / Description: NONE
Crystal growpH: 9 / 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: ID23-1 / Wavelength: 0.9793
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 16, 2015 / Details: BENT CYLINDRICAL MIRRORS
RadiationMonochromator: SINGLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 12860 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 43.18 Å2 / Rmerge(I) obs: 0.2 / Net I/σ(I): 7.2
Reflection shellResolution: 2.75→2.82 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.99 / Mean I/σ(I) obs: 1.1 / % possible all: 85.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.75→41.633 Å / SU ML: 0.39 / σ(F): 1.36 / Phase error: 26.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2496 642 5 %
Rwork0.1992 --
obs0.2018 12849 98.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.75→41.633 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3300 0 74 25 3399
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033466
X-RAY DIFFRACTIONf_angle_d0.6814670
X-RAY DIFFRACTIONf_dihedral_angle_d13.1711284
X-RAY DIFFRACTIONf_chiral_restr0.028456
X-RAY DIFFRACTIONf_plane_restr0.003612
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7499-2.96220.37821160.30592216X-RAY DIFFRACTION91
2.9622-3.26020.33221280.26362425X-RAY DIFFRACTION99
3.2602-3.73170.27581290.20822446X-RAY DIFFRACTION100
3.7317-4.70050.21741310.15952499X-RAY DIFFRACTION100
4.7005-41.63820.19241380.16852621X-RAY DIFFRACTION100

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