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- PDB-4krs: Tankyrase-1 complexed with small molecule inhibitor -

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Basic information

Entry
Database: PDB / ID: 4krs
TitleTankyrase-1 complexed with small molecule inhibitor
ComponentsTankyrase-1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / TRANSFERASE-TRANSFERASE INHIBITOR complex
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 / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / protein localization to chromosome, telomeric region / 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 / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / protein localization to chromosome, telomeric region / protein poly-ADP-ribosylation / pericentriolar material / mitotic spindle pole / NAD+-protein ADP-ribosyltransferase activity / positive regulation of telomere capping / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+-protein poly-ADP-ribosyltransferase activity / 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 / Degradation of AXIN / peptidyl-threonine phosphorylation / Wnt signaling pathway / Regulation of PTEN stability and activity / protein polyubiquitination / protein transport / positive regulation of canonical Wnt signaling pathway / histone binding / peptidyl-serine phosphorylation / nuclear membrane / chromosome, telomeric region / nuclear body / Ub-specific processing proteases / cell division / Golgi membrane / Golgi apparatus / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
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 ...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-1SX / Poly [ADP-ribose] polymerase tankyrase-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.29 Å
AuthorsStams, T. / Kirby, C.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Structure-Efficiency Relationship of [1,2,4]Triazol-3-ylamines as Novel Nicotinamide Isosteres that Inhibit Tankyrases.
Authors: Shultz, M.D. / Majumdar, D. / Chin, D.N. / Fortin, P.D. / Feng, Y. / Gould, T. / Kirby, C.A. / Stams, T. / Waters, N.J. / Shao, W.
History
DepositionMay 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Feb 28, 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_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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_id / _struct_conn.ptnr2_label_asym_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-1
B: Tankyrase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,92111
Polymers50,7052
Non-polymers1,2169
Water2,270126
1
A: Tankyrase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1057
Polymers25,3531
Non-polymers7526
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tankyrase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8174
Polymers25,3531
Non-polymers4643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)124.594, 44.233, 87.845
Angle α, β, γ (deg.)90.00, 90.14, 90.00
Int Tables number5
Space group name H-MC121

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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: 25352.658 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN
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.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-1SX / 4-tert-butyl-N-(5,6-dihydro[1,3]thiazolo[2,3-c][1,2,4]triazol-3-yl)benzamide


Mass: 302.395 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H18N4OS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.39 Å3/Da / Density % sol: 48.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: RESERVOIR SOLUTION: 15% PEG3350, 100MM BIS-TRIS PH 5.8, 320MM AMMONIUM SULFATE. PROTEIN SOLUTION: 20 MG/ML IN 25 MM TRIS PH 8.0, 200MM NACL, 1MM TCEP, 1MM PJ34. EQUAL VOLUMES (2 UL) OF ...Details: RESERVOIR SOLUTION: 15% PEG3350, 100MM BIS-TRIS PH 5.8, 320MM AMMONIUM SULFATE. PROTEIN SOLUTION: 20 MG/ML IN 25 MM TRIS PH 8.0, 200MM NACL, 1MM TCEP, 1MM PJ34. EQUAL VOLUMES (2 UL) OF RESERVIOR SOLUTION AND PROTEIN SOLUTION WERE MIXED AND SET AS HANGING DROPS. CRYSTALS WERE THEN MOVED INTO A SOAKING SOLUTION CONTAINING 18% PEG 3350, 320MM AMMONIUM SULFATE, 100MM BIS-TRIS, 0.2 MM INHIBITOR, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. obs: 21041 / % possible obs: 97.9 % / Redundancy: 3.24 % / Biso Wilson estimate: 38 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 12.47
Reflection shellResolution: 2.29→2.36 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.28 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIXmodel building
PHENIX(phenix.refine)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.29→43.9 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2689 1052 -Random
Rwork0.207 ---
obs0.2102 21041 95.59 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.8165 Å20 Å22.6078 Å2
2--13.6741 Å20 Å2
3----10.8575 Å2
Refinement stepCycle: LAST / Resolution: 2.29→43.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3330 0 69 126 3525
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_deg1.025
X-RAY DIFFRACTIONf_dihedral_angle_d16.19
LS refinement shellResolution: 2.29→2.3909 Å
RfactorNum. reflection% reflection
Rfree0.3655 114 -
Rwork0.251 --
obs-2053 80 %

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