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- PDB-4j3m: Tankyrase 2 in complex with 3-chloro-4-(4-methyl-2-oxo-1,2-dihydr... -

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Basic information

Entry
Database: PDB / ID: 4j3m
TitleTankyrase 2 in complex with 3-chloro-4-(4-methyl-2-oxo-1,2-dihydroquinolin-7-yl)benzoic acid
ComponentsTankyrase-2
KeywordsTRANSFERASE / ribosylation
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 / NAD+-protein mono-ADP-ribosyltransferase activity ...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 / NAD+-protein mono-ADP-ribosyltransferase activity / pericentriolar material / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ poly-ADP-ribosyltransferase activity / positive regulation of telomere maintenance via telomerase / nucleotidyltransferase activity / TCF dependent signaling in response to WNT / Degradation of AXIN / Regulation of PTEN stability and activity / Wnt signaling pathway / 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 / cytoplasm / cytosol
Similarity search - Function
Ankyrin repeat / 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 ...Ankyrin repeat / 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-AJ8 / Poly [ADP-ribose] polymerase tankyrase-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsJansson, A.E. / Larsson, E.A. / Nordlund, P.L.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Fragment-based ligand design of novel potent inhibitors of tankyrases.
Authors: Larsson, E.A. / Jansson, A.E. / Ng, F.M. / Then, S.W. / Panicker, R. / Liu, B. / Sangthongpitag, K. / Pendharkar, V. / Tai, S.J. / Hill, J. / Dan, C. / Ho, S.Y. / Cheong, W.W. / Poulsen, A. ...Authors: Larsson, E.A. / Jansson, A.E. / Ng, F.M. / Then, S.W. / Panicker, R. / Liu, B. / Sangthongpitag, K. / Pendharkar, V. / Tai, S.J. / Hill, J. / Dan, C. / Ho, S.Y. / Cheong, W.W. / Poulsen, A. / Blanchard, S. / Lin, G.R. / Alam, J. / Keller, T.H. / Nordlund, P.
History
DepositionFeb 6, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_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
B: Tankyrase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,22111
Polymers47,9862
Non-polymers1,2359
Water7,494416
1
A: Tankyrase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5645
Polymers23,9931
Non-polymers5714
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tankyrase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6576
Polymers23,9931
Non-polymers6635
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.531, 99.275, 114.652
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
/ NCS ensembles :
ID
1
2

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Components

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Protein , 1 types, 2 molecules AB

#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: 23993.195 Da / Num. of mol.: 2 / Fragment: cataltytic domain, UNP RESIDUES 952-1161
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARP5B, TANK2, TNKL, TNKS2 / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9H2K2, NAD+ ADP-ribosyltransferase

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Non-polymers , 5 types, 425 molecules

#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.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-AJ8 / 3-chloro-4-(4-methyl-2-oxo-1,2-dihydroquinolin-7-yl)benzoic acid


Mass: 313.735 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H12ClNO3
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / 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: 2.65 Å3/Da / Density % sol: 53.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 17% PEG 3350, 0.2M Ammonium sulphate, 0.1M Tris pH 8.5, vapour diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 40482 / Num. obs: 40482 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0032refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
SCALAdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KR7

3kr7


Resolution: 1.9→29.98 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.927 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.704 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2178 1926 5 %RANDOM
Rwork0.1705 ---
obs0.1729 38311 94.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 433.58 Å2 / Biso mean: 23.9644 Å2 / Biso min: 7.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å2-0 Å2
2---0.02 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3322 0 72 416 3810
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0193497
X-RAY DIFFRACTIONr_angle_refined_deg2.21.954722
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2395420
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.60423.073179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.58115568
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4921526
X-RAY DIFFRACTIONr_chiral_restr0.1680.2471
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212776
X-RAY DIFFRACTIONr_mcbond_it2.9242.0181668
X-RAY DIFFRACTIONr_mcangle_it4.3552.9912080
X-RAY DIFFRACTIONr_scbond_it4.2592.4091827
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION / Type: TIGHT THERMAL / Weight position: 0.5

Ens-IDAuth asym-IDNumberRms dev position (Å)
1A16786.89
2B221.81
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 116 -
Rwork0.227 1871 -
all-1987 -
obs--66.68 %

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