[English] 日本語
Yorodumi
- PDB-5zqo: Tankyrase-2 in complex with compound 1a -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5zqo
TitleTankyrase-2 in complex with compound 1a
Components(Tankyrase-2) x 2
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Tankyrase / PARP / ADP-ribosylation / Transferase / Inhibitor / Transferase-transferase inhibitor complex
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
YefM-like fold / YefM-like fold - #10 / Ankyrin repeat / Phosphoenolpyruvate Carboxykinase; domain 3 - #10 / Other non-globular / Phosphoenolpyruvate Carboxykinase; domain 3 / Ankyrin repeats (many copies) / 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 / 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 / Special / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-9GX / Poly [ADP-ribose] polymerase tankyrase-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsNiwa, H. / Shirai, F. / Sato, S. / Yoshimoto, N. / Tsumura, T. / Okue, M. / Shirouzu, M. / Seimiya, H. / Umehara, T.
CitationJournal: J. Med. Chem. / Year: 2019
Title: Discovery of Novel Spiroindoline Derivatives as Selective Tankyrase Inhibitors.
Authors: Shirai, F. / Tsumura, T. / Yashiroda, Y. / Yuki, H. / Niwa, H. / Sato, S. / Chikada, T. / Koda, Y. / Washizuka, K. / Yoshimoto, N. / Abe, M. / Onuki, T. / Mazaki, Y. / Hirama, C. / Fukami, T. ...Authors: Shirai, F. / Tsumura, T. / Yashiroda, Y. / Yuki, H. / Niwa, H. / Sato, S. / Chikada, T. / Koda, Y. / Washizuka, K. / Yoshimoto, N. / Abe, M. / Onuki, T. / Mazaki, Y. / Hirama, C. / Fukami, T. / Watanabe, H. / Honma, T. / Umehara, T. / Shirouzu, M. / Okue, M. / Kano, Y. / Watanabe, T. / Kitamura, K. / Shitara, E. / Muramatsu, Y. / Yoshida, H. / Mizutani, A. / Seimiya, H. / Yoshida, M. / Koyama, H.
History
DepositionApr 19, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)25,3939
Polymers24,5152
Non-polymers8787
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7290 Å2
ΔGint-90 kcal/mol
Surface area10000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.897, 66.897, 117.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-1339-

HOH

-
Components

-
Protein / Protein/peptide , 2 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: 19150.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNKS2, PARP5B, TANK2, TNKL / Plasmid: pCR2.1TOPO / Production host: Cell-free synthesis (others) / References: UniProt: Q9H2K2, NAD+ ADP-ribosyltransferase
#2: Protein/peptide 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: 5364.037 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNKS2, PARP5B, TANK2, TNKL / Plasmid: pCR2.1TOPO / Production host: Cell-free synthesis (others) / References: UniProt: Q9H2K2, NAD+ ADP-ribosyltransferase

-
Non-polymers , 5 types, 159 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Zn / References: NAD+ ADP-ribosyltransferase
#4: Chemical ChemComp-9GX / 2-[4-(2-methoxyphenyl)piperazin-1-yl]-5,6,7,8-tetrahydroquinazolin-4(3H)-one


Mass: 340.419 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H24N4O2
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Bis-Tris pH 6.5, 2% PEG MME 550, 1.8M ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.06→47.3 Å / Num. obs: 17232 / % possible obs: 99.9 % / Redundancy: 14.2 % / CC1/2: 0.998 / Rpim(I) all: 0.042 / Rrim(I) all: 0.158 / Rsym value: 0.152 / Net I/σ(I): 15.1
Reflection shellResolution: 2.06→2.11 Å / Redundancy: 13.9 % / Mean I/σ(I) obs: 2.6 / Num. unique obs: 1285 / CC1/2: 0.8 / Rpim(I) all: 0.31 / Rrim(I) all: 1.166 / Rsym value: 1.123 / % possible all: 99.1

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KR7

3kr7


Resolution: 2.06→47.3 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / Phase error: 19.15
RfactorNum. reflection% reflection
Rfree0.203 866 5.08 %
Rwork0.163 --
obs0.165 17175 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.06→47.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1667 0 53 152 1872
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081760
X-RAY DIFFRACTIONf_angle_d0.7982369
X-RAY DIFFRACTIONf_dihedral_angle_d19.311021
X-RAY DIFFRACTIONf_chiral_restr0.054232
X-RAY DIFFRACTIONf_plane_restr0.005305
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0568-2.12310.27951490.23912666X-RAY DIFFRACTION99
2.1231-2.1990.2821690.21232722X-RAY DIFFRACTION100
2.199-2.28710.26071580.2062711X-RAY DIFFRACTION100
2.2871-2.39120.25991450.19662733X-RAY DIFFRACTION100
2.3912-2.51720.21831620.18612658X-RAY DIFFRACTION100
2.5172-2.67490.25991450.19232768X-RAY DIFFRACTION100
2.6749-2.88140.23191590.16812702X-RAY DIFFRACTION100
2.8814-3.17130.2071260.16412733X-RAY DIFFRACTION100
3.1713-3.63010.18561220.14442735X-RAY DIFFRACTION100
3.6301-4.57290.14391400.12062725X-RAY DIFFRACTION100
4.5729-47.31580.15251250.15032753X-RAY DIFFRACTION100
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)
16.7005-0.8312-4.89642.34490.85033.6174-0.34170.1732-0.5984-0.03220.1212-0.04110.891-0.11740.16510.3989-0.0136-0.0660.2234-0.01310.429310.293347.24378.7199
23.8322.5222-0.03247.59790.3921.3410.09270.3652-0.1895-0.7871-0.10510.08970.2243-0.00610.05820.32640.0717-0.0130.2228-0.0370.220115.534157.39191.3402
33.69751.2051.463.68621.32336.4916-0.0505-0.04410.28620.06220.0989-0.304-0.03390.0149-0.04710.24430.0066-0.00920.15930.02560.259825.410970.87139.8818
47.95222.5253-2.70552.4072-0.75441.9596-0.23920.0915-0.5716-0.20280.045-0.02790.2689-0.15760.16470.27580.0096-0.00350.16850.0320.257713.649953.108710.5268
54.6618-3.10160.59418.4917-1.4213.5624-0.1396-0.1905-0.52330.34390.2851.0046-0.0844-0.9142-0.16470.20510.02270.03340.4681-0.00760.3493-8.037261.921210.9688
62.3039-0.11240.23061.97050.46552.29980.0909-0.016-0.03050.0409-0.00230.0965-0.1865-0.3803-0.11260.22780.0310.01910.21940.01250.19123.643264.114411.7644
73.58631.03481.66288.26981.85082.62780.0502-0.52940.4010.6493-0.15340.4666-0.39220.03180.06690.48230.05530.03570.3023-0.03890.31335.543272.3420.734
81.24610.4908-0.22971.3168-0.09060.6470.0095-0.2564-0.02260.2015-0.0052-0.1347-0.0899-0.0319-0.01090.2730.0279-0.0390.2060.02410.232518.281764.829716.1914
92.54631.7235-1.88323.5973-0.58972.95730.1106-0.39910.45650.50550.02090.3132-0.5528-0.1186-0.09390.4380.16330.04050.38010.01130.34470.625579.371710.4723
103.06490.13610.1171.5053-0.48121.637-0.02520.07940.1566-0.0047-0.0006-0.0245-0.1681-0.09130.01670.28090.0324-0.01910.1875-0.01320.170311.454968.13969.6779
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 952 THROUGH 962 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 963 THROUGH 975 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 976 THROUGH 991 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 992 THROUGH 1002 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 1003 THROUGH 1019 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 1020 THROUGH 1042 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 1043 THROUGH 1058 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 1059 THROUGH 1102 )
9X-RAY DIFFRACTION9(CHAIN 'A' AND (RESID 1103 THROUGH 1113 )) OR (CHAIN 'B' AND (RESID 1115 THROUGH 1123 ))
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 1124 THROUGH 1161 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more