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- PDB-5ax9: Crystal structure of the kinase domain of human TRAF2 and NCK-int... -

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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 / Wnt signaling pathway ...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 / protein autophosphorylation / Oxidative Stress Induced Senescence / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / Rho-dependent protein serine/threonine kinase activity / positive regulation of protein phosphorylation / histone H3T6 kinase activity / histone H2AS1 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / cytoskeleton / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / 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. / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 ...: / Domain found in NIK1-like kinases, mouse citron and yeast ROM1, ROM2 / CNH domain / Citron homology (CNH) domain / Citron homology (CNH) domain profile. / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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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)

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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

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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

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