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- PDB-4pnn: Crystal Structure of human Tankyrase 2 in complex with 4HQN. -

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Basic information

Entry
Database: PDB / ID: 4pnn
TitleCrystal Structure of human Tankyrase 2 in complex with 4HQN.
ComponentsTankyrase-2
KeywordsTRANSFERASE / poly(ADP-ribosylation) polymerase (PARP)
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 / NAD+-protein ADP-ribosyltransferase activity / positive regulation of telomere capping / NAD+ 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 / NAD+-protein ADP-ribosyltransferase activity / positive regulation of telomere capping / NAD+ 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
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. ...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
quinazolin-4(1H)-one / Poly [ADP-ribose] polymerase tankyrase-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.65 Å
AuthorsQiu, W. / Lam, R. / Romanov, V. / Gordon, R. / Gebremeskel, S. / Vodsedalek, J. / Thompson, C. / Beletskaya, I. / Battaile, K.P. / Pai, E.F. / Chirgadze, N.Y.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Insights into the binding of PARP inhibitors to the catalytic domain of human tankyrase-2.
Authors: Qiu, W. / Lam, R. / Voytyuk, O. / Romanov, V. / Gordon, R. / Gebremeskel, S. / Vodsedalek, J. / Thompson, C. / Beletskaya, I. / Battaile, K.P. / Pai, E.F. / Rottapel, R. / Chirgadze, N.Y.
History
DepositionMay 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 7, 2015Group: Database references
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_database_status / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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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
C: Tankyrase-2
D: Tankyrase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,64511
Polymers103,9454
Non-polymers7007
Water17,817989
1
A: Tankyrase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1983
Polymers25,9861
Non-polymers2122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tankyrase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1983
Polymers25,9861
Non-polymers2122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Tankyrase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1983
Polymers25,9861
Non-polymers2122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Tankyrase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0522
Polymers25,9861
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.170, 79.620, 153.180
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsmonomer

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Components

#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: 25986.291 Da / Num. of mol.: 4 / Fragment: PARP, catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNKS2, PARP5B, TANK2, TNKL / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H2K2, NAD+ ADP-ribosyltransferase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-JPZ / quinazolin-4(1H)-one


Mass: 146.146 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H6N2O
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 989 / 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: 2.18 Å3/Da / Density % sol: 43.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M NaCl, 0.1M Sodium, Hepes buffer at pH7.5, 12-15% iso-propanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 12, 2009 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→79.63 Å / Num. obs: 106044 / % possible obs: 96.7 % / Redundancy: 6.73 % / Biso Wilson estimate: 22.33 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 18.91 / Num. measured all: 773310
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. possibleNum. unique obsNet I/σ(I) obs% possible all
1.65-1.674.040.586192119151.7399.7
1.67-1.74.380.582556755411.8699.5
1.7-1.745.20.531684268372.3699.9
1.74-1.786.520.476623062293.13100
1.78-1.827.390.441573057303.78100
1.82-1.877.420.395642464244.22100
1.87-1.945.630.379794561463.6477.4
1.94-27.440.304597459744.92100
2-2.077.440.209612061209.07100
2.07-2.147.410.175370537011.26100
2.14-2.237.460.1625921592110.76100
2.23-2.365.90.1337022563614.5480.3
2.36-2.497.460.0935702570220.1100
2.49-2.657.450.0755511551124.72100
2.65-2.867.450.0585536553630.73100
2.86-3.157.430.0425397539740.31100
3.15-3.617.40.0315433543350.78100
3.61-4.646.680.0265740531463.0192.6
4.64-79.636.810.0245326530864.8399.7

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Processing

Software
NameVersionClassification
XDS2005/3data reduction
BUSTER-TNTBUSTER 2.10.0refinement
PDB_EXTRACT3.14data extraction
BUSTER2.10.0refinement
RefinementResolution: 1.65→76.59 Å / Cor.coef. Fo:Fc: 0.9559 / Cor.coef. Fo:Fc free: 0.9422 / SU R Cruickshank DPI: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.105 / SU Rfree Blow DPI: 0.102 / SU Rfree Cruickshank DPI: 0.098
RfactorNum. reflection% reflectionSelection details
Rfree0.2198 1070 1.01 %RANDOM
Rwork0.1857 ---
obs0.186 105727 96.46 %-
Displacement parametersBiso max: 117.04 Å2 / Biso mean: 29.47 Å2 / Biso min: 11.31 Å2
Baniso -1Baniso -2Baniso -3
1--2.1011 Å20 Å20 Å2
2---1.7444 Å20 Å2
3---3.8455 Å2
Refine analyzeLuzzati coordinate error obs: 0.211 Å
Refinement stepCycle: final / Resolution: 1.65→76.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6498 0 37 989 7524
Biso mean--25.2 40.91 -
Num. residues----806
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2347SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes152HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1013HARMONIC5
X-RAY DIFFRACTIONt_it6737HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion801SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8070SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6737HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg9058HARMONIC21.02
X-RAY DIFFRACTIONt_omega_torsion4.14
X-RAY DIFFRACTIONt_other_torsion15.86
LS refinement shellResolution: 1.65→1.69 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2229 83 1.05 %
Rwork0.2182 7854 -
all0.2183 7937 -
obs--96.46 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0093-0.17520.16040.4443-0.54262.05360.04980.17070.0350.0282-0.0836-0.0268-0.11210.14540.0338-0.0125-0.01040.0035-0.03620.0064-0.067118.754549.3689-1.3451
21.0333-0.14830.16040.7011-0.28331.6964-0.0127-0.181-0.018-0.05980.0369-0.0064-0.0145-0.019-0.0242-0.03270.0076-0.009-0.0351-0.005-0.05917.2638-9.386836.5234
30.9879-0.3884-0.05330.8324-0.18541.3681-0.0058-0.1353-0.007-0.00430.05550.0207-0.05370.0135-0.0497-0.0348-0.0190.0019-0.04160.0011-0.049318.838332.098231.4016
40.8279-0.36890.15010.084-0.16771.5490.0120.16880.06680.0191-0.0801-0.0491-0.07660.13540.06810.0183-0.0497-0.0043-0.0270.0216-0.054418.37818.58594.4112
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A963 - 1161
2X-RAY DIFFRACTION2{ B|* }B955 - 1161
3X-RAY DIFFRACTION3{ C|* }C953 - 1160
4X-RAY DIFFRACTION4{ D|* }D964 - 1160

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