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- PDB-6ra5: Human tnik in complex with compound 9 -

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Basic information

Entry
Database: PDB / ID: 6ra5
TitleHuman tnik in complex with compound 9
ComponentsTRAF2 and NCK-interacting protein kinase
KeywordsTRANSFERASE / KINASE / INHIBITOR / COMPLEX / TNIK
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-JWE / TRAF2 and NCK-interacting protein kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsRead, J.A.
CitationJournal: To Be Published
Title: Tool inhibitors and assays to interrogate the biology of the TRAF2 and NCK interacting kinase
Authors: Read, J.A.
History
DepositionApr 5, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2020Provider: repository / Type: Initial release

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5604
Polymers70,2162
Non-polymers3432
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-19 kcal/mol
Surface area26160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.793, 53.793, 253.363
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein TRAF2 and NCK-interacting protein kinase


Mass: 35108.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNIK, KIAA0551 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UKE5, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-JWE / 5-bromanyl-2-(2-fluoranylpyridin-4-yl)-1,7-naphthyridin-8-amine


Mass: 319.132 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H8BrFN4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 60.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 8% PEG 8K w/v, 0.1M PCTP (pH 8.0), 0.8% ethylene glycol v/v

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.9→45.8 Å / Num. obs: 17691 / % possible obs: 98.9 % / Redundancy: 2.5 % / Χ2: 0.964 / Net I/σ(I): 10.9
Reflection shellResolution: 2.9→3 Å / Num. unique obs: 1355 / CC1/2: 0.644

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Processing

Software
NameClassification
BUSTERrefinement
MOSFLMdata reduction
Aimlessdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→45.8 Å / Cross valid method: FREE R-VALUE /
Num. reflection% reflection
obs86178 98.9 %
Refinement stepCycle: LAST / Resolution: 2.9→45.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4311 0 20 53 4384

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