[English] 日本語
Yorodumi
- PDB-5ety: Crystal Structure of human Tankyrase-1 bound to K-756 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ety
TitleCrystal Structure of human Tankyrase-1 bound to K-756
ComponentsTankyrase-1
KeywordsTRANSFERASE / Tankyrase / inhibitor / non-competitive / Wnt signal
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 / protein localization to chromosome, telomeric region / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / 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 / protein localization to chromosome, telomeric region / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / protein poly-ADP-ribosylation / pericentriolar material / mitotic spindle pole / NAD+-protein ADP-ribosyltransferase activity / positive regulation of telomere capping / NAD+ ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / mRNA transport / spindle assembly / nuclear pore / positive regulation of telomerase activity / 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 / positive regulation of canonical Wnt signaling pathway / protein transport / 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 / cytosol / cytoplasm
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-K56 / Poly [ADP-ribose] polymerase tankyrase-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsTakahashi, Y. / Miyagi, H. / Suzuki, M. / Saito, J.
CitationJournal: Mol.Cancer Ther. / Year: 2016
Title: The Discovery and Characterization of K-756, a Novel Wnt/ beta-Catenin Pathway Inhibitor Targeting Tankyrase
Authors: Okada-Iwasaki, R. / Takahashi, Y. / Watanabe, Y. / Ishida, H. / Saito, J. / Nakai, R. / Asai, A.
History
DepositionNov 18, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Database references
Revision 1.2Feb 19, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tankyrase-1
B: Tankyrase-1
C: Tankyrase-1
D: Tankyrase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,15112
Polymers117,1564
Non-polymers1,9968
Water1,33374
1
A: Tankyrase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7883
Polymers29,2891
Non-polymers4992
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tankyrase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7883
Polymers29,2891
Non-polymers4992
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Tankyrase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7883
Polymers29,2891
Non-polymers4992
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Tankyrase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7883
Polymers29,2891
Non-polymers4992
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)158.846, 74.680, 84.603
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 0 / Auth seq-ID: 1105 - 1314 / Label seq-ID: 38 - 247

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

-
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: 29288.953 Da / Num. of mol.: 4 / Fragment: UNP residues 1091-1324 / Mutation: M1266L
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.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-K56 / 3-[[1-(6,7-dimethoxyquinazolin-4-yl)piperidin-4-yl]methyl]-1,4-dihydroquinazolin-2-one


Mass: 433.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H27N5O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.14 Å3/Da / Density % sol: 42.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.8 / Details: 0.1M Na-Succinate pH 5.8, 6% PEG MME 5000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 29, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 21422 / % possible obs: 93.8 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.137 / Χ2: 1.516 / Net I/av σ(I): 12.038 / Net I/σ(I): 7.8 / Num. measured all: 84084
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.9-33.70.8719901.10489.1
3-3.123.70.43219971.1789
3.12-3.273.80.19819751.33488.7
3.27-3.443.80.13520081.35189.6
3.44-3.653.80.12520911.42791.8
3.65-3.943.90.13321311.62794.4
3.94-4.3340.13522201.87997.3
4.33-4.964.20.12323011.89499.7
4.96-6.244.20.11423121.63799.7
6.24-5040.08423971.47197.8

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0071refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→50 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.883 / SU B: 48.765 / SU ML: 0.411 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.539 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.3054 1098 5.2 %RANDOM
Rwork0.255 ---
obs0.2576 20069 91.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 110.29 Å2 / Biso mean: 55.05 Å2 / Biso min: 17.41 Å2
Baniso -1Baniso -2Baniso -3
1--1.38 Å2-0 Å2-0 Å2
2--0.63 Å2-0 Å2
3---0.75 Å2
Refinement stepCycle: final / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6571 0 132 74 6777
Biso mean--42.02 32.06 -
Num. residues----817
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0196880
X-RAY DIFFRACTIONr_bond_other_d0.0050.026330
X-RAY DIFFRACTIONr_angle_refined_deg1.4911.9529265
X-RAY DIFFRACTIONr_angle_other_deg1.079314506
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7675806
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.70322.978356
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.56151128
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3151553
X-RAY DIFFRACTIONr_chiral_restr0.10.2922
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027851
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021786
X-RAY DIFFRACTIONr_mcbond_it1.3082.3453257
X-RAY DIFFRACTIONr_mcbond_other1.3082.3453256
X-RAY DIFFRACTIONr_mcangle_it2.33.5114052
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A115890.07
12B115890.07
21A115190.08
22C115190.08
31A115750.09
32D115750.09
41B113790.07
42C113790.07
51B113410.08
52D113410.08
61C118000.06
62D118000.06
LS refinement shellResolution: 2.898→2.973 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.578 55 -
Rwork0.579 1132 -
all-1187 -
obs--71.29 %
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)
15.5266-0.1079-0.05751.2563-0.26293.37350.00510.00070.22820.17410.02560.022-0.22820.0378-0.03080.0381-0.0249-0.00450.60480.00340.0623-36.56319.49-16.37
26.7109-0.0860.33921.47430.34723.2198-0.07730.29830.4286-0.20890.0426-0.0784-0.14-0.04670.03470.0572-0.045-0.01230.42170.0410.0782-82.75418.7-26.023
34.7939-0.5406-0.29261.41870.20692.6546-0.0588-0.2473-0.08030.08920.0204-0.07480.0564-0.17940.03840.00790.02310.00130.71860.02970.0278-81.66619.46-55.234
45.2754-0.6613-0.14851.28350.05432.6338-0.0596-0.186-0.01560.15860.013-0.0584-0.0065-0.03070.04660.0223-0.01080.00370.5694-0.02540.0559-41.796-17.12-13.001
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1105 - 1314
2X-RAY DIFFRACTION2B1105 - 1314
3X-RAY DIFFRACTION3C1105 - 1314
4X-RAY DIFFRACTION4D1105 - 1314

+
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