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- PDB-7orf: Crystal structure of JNK3 in complex with FMU-001-367 (compound 1) -

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Basic information

Entry
Database: PDB / ID: 7orf
TitleCrystal structure of JNK3 in complex with FMU-001-367 (compound 1)
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 / cytoplasm / cytosol
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-0G3 / Mitogen-activated protein kinase 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsChaikuad, A. / Koch, P. / Laufer, S. / 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)44,16423
Polymers42,1471
Non-polymers2,01722
Water6,251347
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint58 kcal/mol
Surface area16680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.849, 71.170, 108.090
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-0G3 / N-[4-[[4-[5-(4-fluorophenyl)-3-methyl-2-methylsulfanyl-imidazol-4-yl]pyridin-2-yl]amino]phenyl]-3-(propanoylamino)benzamide


Mass: 580.675 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H29FN6O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / 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: 2.5 Å3/Da / Density % sol: 50.86 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 34% PEG400 and 0.1 M MES, pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.7→30.11 Å / Num. obs: 47324 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.045 / Rrim(I) all: 0.115 / Net I/av σ(I): 12 / Net I/σ(I): 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.7-1.796.10.817268100.6690.3910.983100
5.38-30.116.30.03216490.9990.0140.03599.3

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4x21

4x21


Resolution: 1.7→30.11 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.532 / SU ML: 0.075 / SU R Cruickshank DPI: 0.0942 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2046 2352 5 %RANDOM
Rwork0.167 ---
obs0.1689 44907 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 84.31 Å2 / Biso mean: 25.265 Å2 / Biso min: 12.29 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å2-0 Å20 Å2
2---0.48 Å2-0 Å2
3----0.22 Å2
Refinement stepCycle: final / Resolution: 1.7→30.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2821 0 134 347 3302
Biso mean--33.07 35.4 -
Num. residues----351
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193064
X-RAY DIFFRACTIONr_bond_other_d0.0020.022914
X-RAY DIFFRACTIONr_angle_refined_deg1.5891.9774123
X-RAY DIFFRACTIONr_angle_other_deg0.92636766
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.475369
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.00224.179134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.20515536
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3841518
X-RAY DIFFRACTIONr_chiral_restr0.1060.2447
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213487
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02599
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 168 -
Rwork0.285 3260 -
all-3428 -
obs--99.97 %
Refinement TLS params.Method: refined / Origin x: 54.495 Å / Origin y: 6.501 Å / Origin z: 21.835 Å
111213212223313233
T0.0964 Å2-0.0011 Å2-0.0001 Å2-0.001 Å2-0.0008 Å2--0.0032 Å2
L0.1011 °2-0.0595 °2-0.0102 °2-0.3751 °20.1024 °2--0.3269 °2
S-0.0113 Å °0.0095 Å °-0.0109 Å °0.0141 Å °-0.0057 Å °0.0305 Å °-0.0013 Å °0.006 Å °0.0171 Å °

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