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- PDB-8vnx: A structural study of selectivity mechanisms for JNK3 and p38 alp... -

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Basic information

Entry
Database: PDB / ID: 8vnx
TitleA structural study of selectivity mechanisms for JNK3 and p38 alpha with indazole scaffold probing compounds
ComponentsMitogen-activated protein kinase 10
KeywordsTRANSFERASE / C-Jun terminal kinase 3 / JNK3 / p38 alpha / Kinase / selectivity
Function / homology
Function and homology information


Activation of the AP-1 family of transcription factors / Fc-epsilon receptor signaling pathway / MAP kinase kinase activity / response to light stimulus / JUN kinase activity / mitogen-activated protein kinase / JNK cascade / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / FCERI mediated MAPK activation / regulation of circadian rhythm ...Activation of the AP-1 family of transcription factors / Fc-epsilon receptor signaling pathway / MAP kinase kinase activity / response to light stimulus / JUN kinase activity / mitogen-activated protein kinase / JNK cascade / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / FCERI mediated MAPK activation / regulation of circadian rhythm / cellular senescence / rhythmic process / Oxidative Stress Induced Senescence / protein phosphorylation / protein serine kinase activity / signal transduction / mitochondrion / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Mitogen-activated protein (MAP) kinase, JNK / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-WHQ / Mitogen-activated protein kinase 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPark, H. / Feng, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA) United States
CitationJournal: To Be Published
Title: A structural study of selectivity mechanisms for JNK3 and p38 alpha with indazole scaffold probing compounds
Authors: Park, H. / Feng, Y.
History
DepositionJan 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitogen-activated protein kinase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0942
Polymers52,6491
Non-polymers4451
Water2,396133
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.220, 71.210, 107.740
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Mitogen-activated protein kinase 10 / MAPK 10 / MAP kinase p49 3F12 / Stress-activated protein kinase 1b / SAPK1b / Stress-activated ...MAPK 10 / MAP kinase p49 3F12 / Stress-activated protein kinase 1b / SAPK1b / Stress-activated protein kinase JNK3 / c-Jun N-terminal kinase 3


Mass: 52649.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK10, JNK3, JNK3A, PRKM10, SAPK1B / Production host: Escherichia coli (E. coli)
References: UniProt: P53779, mitogen-activated protein kinase
#2: Chemical ChemComp-WHQ / (4P)-4-[5-(2-chloro-6-fluoroanilino)-6-(methoxymethyl)-1H-indazol-1-yl]-N-methylthiophene-2-carboxamide


Mass: 444.910 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H18ClFN4O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 1.9 Å3/Da / Density meas: 35.38 Mg/m3 / Density % sol: 35.34 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion / Details: 0.2 M ammonium tartrate pH 7.2, 18 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→37.49 Å / Num. obs: 27866 / % possible obs: 99.6 % / Redundancy: 6 % / Biso Wilson estimate: 28.04 Å2 / CC1/2: 0.99 / Net I/σ(I): 4
Reflection shellResolution: 2→2.06 Å / Num. unique obs: 2572 / CC1/2: 0.76

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→37.49 Å / SU ML: 0.219 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.7359
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2557 1406 5.05 %
Rwork0.2119 26433 -
obs0.2141 27839 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.53 Å2
Refinement stepCycle: LAST / Resolution: 2→37.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2796 0 30 133 2959
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00382902
X-RAY DIFFRACTIONf_angle_d0.72823933
X-RAY DIFFRACTIONf_chiral_restr0.0441430
X-RAY DIFFRACTIONf_plane_restr0.0074501
X-RAY DIFFRACTIONf_dihedral_angle_d16.44591093
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.070.31191550.25192566X-RAY DIFFRACTION99.63
2.07-2.150.2951490.24242592X-RAY DIFFRACTION99.75
2.15-2.250.29941250.23382638X-RAY DIFFRACTION99.75
2.25-2.370.28161240.24042603X-RAY DIFFRACTION99.13
2.37-2.510.24171430.23442596X-RAY DIFFRACTION98.85
2.51-2.710.29531390.23332645X-RAY DIFFRACTION99.93
2.71-2.980.30841340.23932654X-RAY DIFFRACTION99.71
2.98-3.410.26561320.2232658X-RAY DIFFRACTION98.97
3.41-4.30.23811340.18852689X-RAY DIFFRACTION99.19
4.3-37.490.21241710.18192792X-RAY DIFFRACTION99.26

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