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- PDB-7ore: Crystal structure of JNK3 in complex with light-activated covalen... -

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Basic information

Entry
Database: PDB / ID: 7ore
TitleCrystal structure of JNK3 in complex with light-activated covalent inhibitor MR-II-249 with both non-covalent and covalent binding modes (compound 4)
ComponentsMitogen-activated protein kinase 10
KeywordsTRANSFERASE / kinase / MAPK / MAPK10 / light activation / covalent inhibitor / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


JUN kinase activity / Activation of the AP-1 family of transcription factors / Fc-epsilon receptor signaling pathway / MAP kinase kinase activity / response to light stimulus / 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 ...JUN kinase activity / Activation of the AP-1 family of transcription factors / Fc-epsilon receptor signaling pathway / MAP kinase kinase activity / response to light stimulus / 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-0EI / Mitogen-activated protein kinase 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsChaikuad, A. / Reynders, M. / Trauner, D. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: Controlling the Covalent Reactivity of a Kinase Inhibitor with Light.
Authors: Reynders, M. / Chaikuad, A. / Berger, B.T. / Bauer, K. / Koch, P. / Laufer, S. / Knapp, S. / Trauner, D.
History
DepositionJun 5, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 15, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)44,00312
Polymers42,1471
Non-polymers1,85611
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint24 kcal/mol
Surface area17180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.868, 71.059, 107.456
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 42146.750 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 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -R3-pRARE2
References: UniProt: P53779, mitogen-activated protein kinase
#2: Chemical ChemComp-0EI / 4-(dimethylamino)-N-[(5Z)-9-[[4-[5-(4-fluorophenyl)-3-methyl-2-methylsulfanyl-imidazol-4-yl]pyridin-2-yl]amino]-11,12-dihydrobenzo[c][1,2]benzodiazocin-2-yl]butanamide


Mass: 648.795 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C36H37FN8OS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.39 Å3/Da / Density % sol: 48.63 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 16% medium-molecular weight PEG smears (MMW PEG Smears) and 0.1 M HEPES, pH 7.8

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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 PILATUS3 6M / Detector: PIXEL / Date: Jul 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.18→29.65 Å / Num. obs: 21811 / % possible obs: 99.9 % / Redundancy: 7.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.044 / Rrim(I) all: 0.118 / Net I/av σ(I): 10.6 / Net I/σ(I): 10.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.18-2.37.10.9032.131340.8760.3931.05999.9
6.89-29.656.30.0537800.9970.0220.05799

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Processing

Software
NameVersionClassification
Aimless0.7.2data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4x21

4x21


Resolution: 2.18→29.65 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.915 / SU B: 16.962 / SU ML: 0.203 / SU R Cruickshank DPI: 0.2906 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.291 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2759 1096 5 %RANDOM
Rwork0.2159 ---
obs0.2189 20663 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 115.9 Å2 / Biso mean: 54.154 Å2 / Biso min: 31.22 Å2
Baniso -1Baniso -2Baniso -3
1-4.27 Å20 Å20 Å2
2---1.89 Å20 Å2
3----2.37 Å2
Refinement stepCycle: final / Resolution: 2.18→29.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2837 0 177 56 3070
Biso mean--54.15 50.7 -
Num. residues----352
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0133092
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172886
X-RAY DIFFRACTIONr_angle_refined_deg1.2741.6544178
X-RAY DIFFRACTIONr_angle_other_deg1.0851.6226681
X-RAY DIFFRACTIONr_dihedral_angle_1_deg18.6735.41366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.50622.617149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.29315517
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5131517
X-RAY DIFFRACTIONr_chiral_restr0.0460.2378
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024220
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02635
LS refinement shellResolution: 2.18→2.236 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 78 -
Rwork0.315 1482 -
all-1560 -
obs--99.94 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.49311.26670.03147.7350.27797.9912-0.04990.2167-0.16840.07460.09840.58590.1353-0.6065-0.04850.22180.0393-0.0220.0659-0.00240.063.14326.79544.767
20.63770.4523-0.95331.5189-1.38524.1710.0018-0.0067-0.14920.0232-0.0422-0.00790.1528-0.00190.04040.2128-0.011-0.02380.0141-0.00720.06299.9719.88629.468
31.07480.7459-1.1852.5633-0.93343.1812-0.03790.0696-0.1625-0.33440.0294-0.04310.25250.01440.00850.2760.00940.01680.009-0.01930.049110.90817.33411.975
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A44 - 93
2X-RAY DIFFRACTION2A94 - 227
3X-RAY DIFFRACTION3A228 - 402

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