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- PDB-4hmh: Crystal structure of tankyrase 2 in complex with 7,3-dihydroxyflavone -

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Basic information

Entry
Database: PDB / ID: 4hmh
TitleCrystal structure of tankyrase 2 in complex with 7,3-dihydroxyflavone
Components(Tankyrase-2) x 2
KeywordsTRANSFERASE / PROTEIN-LIGAND COMPLEX / DIPHTHERIA TOXIN LIKE FOLD / ADP-RIBOSYLATION
Function / homology
Function and homology information


XAV939 stabilizes AXIN / positive regulation of telomere capping / 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 / NAD+-protein mono-ADP-ribosyltransferase activity / NAD+ poly-ADP-ribosyltransferase activity ...XAV939 stabilizes AXIN / positive regulation of telomere capping / 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 / 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 / nucleus / metal ion binding / 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. ...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 / Ankyrin repeat / Special / Ankyrin repeat-containing domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
7-hydroxy-2-(3-hydroxyphenyl)-4H-chromen-4-one / DI(HYDROXYETHYL)ETHER / Poly [ADP-ribose] polymerase tankyrase-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsNarwal, M. / Haikarainen, T. / Lehtio, L.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Screening and structural analysis of flavones inhibiting tankyrases.
Authors: Narwal, M. / Haikarainen, T. / Fallarero, A. / Vuorela, P.M. / Lehtio, L.
History
DepositionOct 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1May 8, 2013Group: Database references
Revision 1.2May 22, 2013Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / software / struct_conn / struct_ref_seq_dif / 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 / _software.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Tankyrase-2
C: Tankyrase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0288
Polymers27,3182
Non-polymers7106
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5880 Å2
ΔGint-34 kcal/mol
Surface area10820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.294, 67.294, 117.005
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AC

#1: Protein Tankyrase-2 / TANK2 / ADP-ribosyltransferase diphtheria toxin-like 6 / ARTD6 / Poly [ADP-ribose] polymerase 5B / ...TANK2 / ADP-ribosyltransferase diphtheria toxin-like 6 / ARTD6 / 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.: 1 / Fragment: C-terminal fragment, UNP residues 946-1113
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNKS2, PARP5B, TANK2, TNKL / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3) / References: UniProt: Q9H2K2, NAD+ ADP-ribosyltransferase
#2: Protein/peptide Tankyrase-2


Mass: 5493.216 Da / Num. of mol.: 1 / Fragment: C-terminal fragment, UNP residues 1114-1162
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNKS2, PARP5B, TANK2, TNKL / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3) / References: UniProt: Q9H2K2, NAD+ ADP-ribosyltransferase

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Non-polymers , 6 types, 45 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-F94 / 7-hydroxy-2-(3-hydroxyphenyl)-4H-chromen-4-one / 7,3-dihydroxyflavone


Mass: 254.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H10O4
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsAUTHOR STATES THAT THE BACTERIAL EXPRESSED TANKYRASE 2 CATALYTIC DOMAIN (UNP RESIDUES 946-1162) WAS ...AUTHOR STATES THAT THE BACTERIAL EXPRESSED TANKYRASE 2 CATALYTIC DOMAIN (UNP RESIDUES 946-1162) WAS CLEAVED WITH CHYMOTRYPSIN PRODUCING TWO POLYPEPTIDES OF RESIDUES 946-1113(CHAIN A) AND RESIDUES 1114-1162(CHAIN C).

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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: 2.42 Å3/Da / Density % sol: 49.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M LiSO4, 0.1 M Tris HCl 24 % PEG3350 , pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.54058 Å
DetectorType: Platinum 135 CCD / Detector: CCD / Date: Jun 29, 2012
RadiationMonochromator: Helios MX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54058 Å / Relative weight: 1
ReflectionResolution: 2.3→58.33 Å / Num. obs: 12517 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.47 % / Rmerge(I) obs: 0.1475 / Net I/σ(I): 8.63
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 2.75 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.64 / Num. unique all: 2082 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PROTEUM2data collection
MOLREPphasing
REFMAC5.6.0117refinement
SAINTdata reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U9H

3u9h


Resolution: 2.3→58.33 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.881 / SU B: 7.039 / SU ML: 0.166 / Cross valid method: THROUGHOUT / ESU R: 0.346 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26201 1183 9.9 %RANDOM
Rwork0.20838 ---
all0.21376 10738 --
obs0.21376 10738 94.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.211 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20 Å20 Å2
2--0.42 Å20 Å2
3----0.85 Å2
Refinement stepCycle: LAST / Resolution: 2.3→58.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1669 0 43 39 1751
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191752
X-RAY DIFFRACTIONr_bond_other_d0.0010.021217
X-RAY DIFFRACTIONr_angle_refined_deg1.5271.9522356
X-RAY DIFFRACTIONr_angle_other_deg0.883.0022923
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0735206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.20322.88990
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.63315286
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6881514
X-RAY DIFFRACTIONr_chiral_restr0.0820.2234
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211958
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02392
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 84 -
Rwork0.276 681 -
obs--95.86 %

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