[English] 日本語
Yorodumi
- PDB-5ax9: Crystal structure of the kinase domain of human TRAF2 and NCK-int... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ax9
TitleCrystal structure of the kinase domain of human TRAF2 and NCK-interacting protein kinase in complex with compund 9
ComponentsTRAF2 and NCK-interacting protein kinase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Inhibitor / kinase / Complex / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


microvillus assembly / : / regulation of dendrite morphogenesis / regulation of MAPK cascade / postsynaptic density, intracellular component / cytoskeleton organization / neuron projection morphogenesis / protein localization to plasma membrane / positive regulation of JNK cascade / recycling endosome ...microvillus assembly / : / regulation of dendrite morphogenesis / regulation of MAPK cascade / postsynaptic density, intracellular component / cytoskeleton organization / neuron projection morphogenesis / protein localization to plasma membrane / positive regulation of JNK cascade / recycling endosome / Wnt signaling pathway / MAPK cascade / presynapse / actin cytoskeleton organization / Oxidative Stress Induced Senescence / protein autophosphorylation / cytoskeleton / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / positive regulation of protein phosphorylation / apical plasma membrane / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Domain found in NIK1-like kinases, mouse citron and yeast ROM1, ROM2 / CNH domain / Citron homology (CNH) domain / Citron homology (CNH) domain profile. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site ...: / Domain found in NIK1-like kinases, mouse citron and yeast ROM1, ROM2 / CNH domain / Citron homology (CNH) domain / Citron homology (CNH) domain profile. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-4KT / TRAF2 and NCK-interacting protein kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsOhbayashi, N. / Kukimoto-Niino, M. / Yamada, T. / Shirouzu, M.
CitationJournal: Nat Commun / Year: 2016
Title: TNIK inhibition abrogates colorectal cancer stemness
Authors: Masuda, M. / Uno, Y. / Ohbayashi, N. / Ohata, H. / Mimata, A. / Kukimoto-Niino, M. / Moriyama, H. / Kashimoto, S. / Inoue, T. / Goto, N. / Okamoto, K. / Shirouzu, M. / Sawa, M. / Yamada, T.
History
DepositionJul 21, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Feb 26, 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 1.3Nov 8, 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: TRAF2 and NCK-interacting protein kinase
B: TRAF2 and NCK-interacting protein kinase
C: TRAF2 and NCK-interacting protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,6718
Polymers105,2293
Non-polymers1,4425
Water1,928107
1
A: TRAF2 and NCK-interacting protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5893
Polymers35,0761
Non-polymers5132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TRAF2 and NCK-interacting protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5893
Polymers35,0761
Non-polymers5132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: TRAF2 and NCK-interacting protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4932
Polymers35,0761
Non-polymers4161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.178, 123.204, 157.652
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

-
Components

#1: Protein TRAF2 and NCK-interacting protein kinase


Mass: 35076.328 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNIK, KIAA0551 / Production host: Baculovirus expression vector pFastBac1-HM
References: UniProt: Q9UKE5, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-4KT / 4-methoxy-3-[2-[(3-methoxy-4-morpholin-4-yl-phenyl)amino]pyridin-4-yl]benzenecarbonitrile


Mass: 416.472 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H24N4O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.5 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 24% PEG3350, 0.2M ammonium sulfate, 0.1M Bis-tris (5.6)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→48.54 Å / Num. obs: 36951 / % possible obs: 100 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.131 / Net I/σ(I): 12.2
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 2.9 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2X7F

2x7f


Resolution: 2.4→48.538 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.99 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2714 1851 5.02 %Random selection
Rwork0.2045 ---
obs0.2079 36883 99.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→48.538 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6711 0 103 107 6921
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066969
X-RAY DIFFRACTIONf_angle_d0.9829407
X-RAY DIFFRACTIONf_dihedral_angle_d15.2222629
X-RAY DIFFRACTIONf_chiral_restr0.0391007
X-RAY DIFFRACTIONf_plane_restr0.0051199
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.46490.35581320.25462656X-RAY DIFFRACTION100
2.4649-2.53740.27981360.23912655X-RAY DIFFRACTION100
2.5374-2.61930.34011340.23662665X-RAY DIFFRACTION100
2.6193-2.71290.31991420.22962618X-RAY DIFFRACTION100
2.7129-2.82150.30791460.2352671X-RAY DIFFRACTION100
2.8215-2.94990.30491280.23582702X-RAY DIFFRACTION100
2.9499-3.10540.32761370.2252657X-RAY DIFFRACTION100
3.1054-3.30.2771370.21782676X-RAY DIFFRACTION100
3.3-3.55470.30211460.20232677X-RAY DIFFRACTION100
3.5547-3.91230.24171610.18482697X-RAY DIFFRACTION100
3.9123-4.4780.21261340.17562711X-RAY DIFFRACTION100
4.478-5.64050.23831560.17972741X-RAY DIFFRACTION100
5.6405-48.54810.27281620.20162906X-RAY DIFFRACTION100

+
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