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- PDB-5d7a: Crystal structure of the kinase domain of TRAF2 and NCK-interacti... -

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Basic information

Entry
Database: PDB / ID: 5d7a
TitleCrystal structure of the kinase domain of TRAF2 and NCK-interacting protein kinase with NCB-0846
ComponentsTRAF2 and NCK-interacting protein kinase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Kinase / 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 / protein phosphorylation / apical plasma membrane / 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-58C / TRAF2 and NCK-interacting protein kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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
DepositionAug 13, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references / Structure summary
Revision 1.2Sep 28, 2016Group: Structure summary
Revision 1.3Feb 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 1.4Nov 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)106,6439
Polymers105,2293
Non-polymers1,4146
Water1267
1
A: TRAF2 and NCK-interacting protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5483
Polymers35,0761
Non-polymers4712
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)35,4522
Polymers35,0761
Non-polymers3751
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)35,6444
Polymers35,0761
Non-polymers5683
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)212.620, 124.972, 49.897
Angle α, β, γ (deg.)90.00, 96.32, 90.00
Int Tables number5
Space group name H-MC121

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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-58C / cis-4-{[2-(1H-benzimidazol-5-ylamino)quinazolin-8-yl]oxy}cyclohexanol


Mass: 375.424 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H21N5O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 3.13 Å3/Da / Density % sol: 60.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2M Ammonium sulfate 0.1M Bis-tris (5.6) 15% PEG3350 7% Ethyleneglycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→46.92 Å / Num. obs: 28803 / % possible obs: 100 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 15.8
Reflection shellResolution: 2.9→3.08 Å / Redundancy: 7.8 % / Mean I/σ(I) obs: 2.7 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2X7F

2x7f


Resolution: 2.9→46.92 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2391 1426 4.95 %
Rwork0.1842 --
obs0.1868 28789 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→46.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6915 0 99 7 7021
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047179
X-RAY DIFFRACTIONf_angle_d0.8229703
X-RAY DIFFRACTIONf_dihedral_angle_d13.9722711
X-RAY DIFFRACTIONf_chiral_restr0.0321042
X-RAY DIFFRACTIONf_plane_restr0.0031239
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.00360.36921190.29722750X-RAY DIFFRACTION100
3.0036-3.12390.31561490.25112765X-RAY DIFFRACTION100
3.1239-3.2660.27751660.22532653X-RAY DIFFRACTION100
3.266-3.43820.28351780.20672687X-RAY DIFFRACTION100
3.4382-3.65350.20861710.18692684X-RAY DIFFRACTION100
3.6535-3.93540.25351290.17842751X-RAY DIFFRACTION100
3.9354-4.33120.21711300.16462750X-RAY DIFFRACTION100
4.3312-4.95740.20791260.16032769X-RAY DIFFRACTION100
4.9574-6.24350.27371370.18552761X-RAY DIFFRACTION100
6.2435-46.93060.18291210.15982793X-RAY DIFFRACTION100

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