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- PDB-3p0n: Human Tankyrase 2 - Catalytic PARP domain in complex with an inhibitor -

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Basic information

Entry
Database: PDB / ID: 3p0n
TitleHuman Tankyrase 2 - Catalytic PARP domain in complex with an inhibitor
ComponentsTankyrase-2
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / PROTEIN-LIGAND COMPLEX / Structural Genomics / Structural Genomics Consortium / SGC / diphtheria toxin like fold / Transferase / NAD+ / ADP-ribosylation / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


XAV939 stabilizes AXIN / positive regulation of telomere capping / NAD+ ADP-ribosyltransferase / protein auto-ADP-ribosylation / protein localization to chromosome, telomeric region / negative regulation of telomere maintenance via telomere lengthening / 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 / protein auto-ADP-ribosylation / protein localization to chromosome, telomeric region / negative regulation of telomere maintenance via telomere lengthening / 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 / nuclear envelope / positive regulation of canonical Wnt signaling pathway / 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 / 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
7-bromopyrrolo[1,2-a]quinoxalin-4(5H)-one / Poly [ADP-ribose] polymerase tankyrase-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKarlberg, T. / Siponen, M.I. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. ...Karlberg, T. / Siponen, M.I. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / Kotenyova, T. / Kouznetsova, E. / Moche, M. / Nordlund, P. / Nyman, T. / Persson, C. / Schutz, P. / Sehic, A. / Thorsell, A.G. / Tresaugues, L. / Van Den Berg, S. / Wahlberg, E. / Weigelt, J. / Welin, M. / Schuler, H. / Structural Genomics Consortium (SGC)
CitationJournal: Nat.Biotechnol. / Year: 2012
Title: Family-wide chemical profiling and structural analysis of PARP and tankyrase inhibitors
Authors: Wahlberg, E. / Karlberg, T. / Kouznetsova, E. / Markova, N. / Macchiarulo, A. / Thorsell, A.G. / Pol, E. / Frostell, A. / Ekblad, T. / Kull, B. / Robertson, G.M. / Pellicciari, R. / Schuler, H. / Weigelt, J.
History
DepositionSep 29, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 20, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 7, 2012Group: Database references
Revision 1.3Jun 19, 2013Group: Database references
Revision 1.4Nov 1, 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_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_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_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_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)55,82912
Polymers54,6002
Non-polymers1,22910
Water8,809489
1
A: Tankyrase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9166
Polymers27,3001
Non-polymers6175
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Tankyrase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9126
Polymers27,3001
Non-polymers6135
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.300, 98.214, 118.684
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-66-

HOH

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Components

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Protein , 1 types, 2 molecules AC

#1: Protein Tankyrase-2 / Poly(ADP-ribose) polymerase / TANK2 / Tankyrase II / TNKS-2 / TRF1-interacting ankyrin-related ADP- ...Poly(ADP-ribose) polymerase / TANK2 / Tankyrase II / TNKS-2 / TRF1-interacting ankyrin-related ADP-ribose polymerase 2 / Tankyrase-like protein / Tankyrase-related protein / Poly [ADP-ribose] polymerase 5B


Mass: 27299.764 Da / Num. of mol.: 2 / Fragment: Catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNKS2 / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) R3 pRARE / References: UniProt: Q9H2K2, NAD+ ADP-ribosyltransferase

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Non-polymers , 5 types, 499 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-BPU / 7-bromopyrrolo[1,2-a]quinoxalin-4(5H)-one


Mass: 263.090 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H7BrN2O
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 489 / 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: 2.44 Å3/Da / Density % sol: 49.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 21% PEG3350, 0.2M ammonium sulfate, 0.1M Tris-HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97908 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 17, 2009 / Details: mirrors
RadiationMonochromator: Si(311) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97908 Å / Relative weight: 1
ReflectionResolution: 1.9→45.38 Å / Num. all: 42208 / Num. obs: 42208 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.062 / Rsym value: 0.04 / Net I/σ(I): 23.7
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.183 / Mean I/σ(I) obs: 10.2 / Num. unique all: 3067 / Rsym value: 0.124 / % possible all: 99.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KR7

3kr7


Resolution: 1.9→45.38 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.401 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19501 2111 5 %RANDOM
Rwork0.15953 ---
all0.16135 40097 --
obs0.16135 40097 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.627 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.74 Å20 Å2
3---0.78 Å2
Refinement stepCycle: LAST / Resolution: 1.9→45.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3333 0 63 489 3885
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0213493
X-RAY DIFFRACTIONr_bond_other_d0.0010.022421
X-RAY DIFFRACTIONr_angle_refined_deg1.7371.9474709
X-RAY DIFFRACTIONr_angle_other_deg0.933.0015805
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1585415
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.57222.857182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.27715576
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9921529
X-RAY DIFFRACTIONr_chiral_restr0.1020.2463
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023914
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02773
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.151.52051
X-RAY DIFFRACTIONr_mcbond_other0.3321.5856
X-RAY DIFFRACTIONr_mcangle_it2.09623285
X-RAY DIFFRACTIONr_scbond_it3.19731442
X-RAY DIFFRACTIONr_scangle_it5.1354.51422
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.901→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.212 153 -
Rwork0.189 2910 -
obs--100 %

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