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- PDB-1pmv: The structure of JNK3 in complex with a dihydroanthrapyrazole inh... -

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Basic information

Entry
Database: PDB / ID: 1pmv
TitleThe structure of JNK3 in complex with a dihydroanthrapyrazole inhibitor
ComponentsMitogen-activated protein kinase 10
KeywordsTRANSFERASE / MAP kinase / apoptosis / inhibition / selectivity
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. / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...Mitogen-activated protein (MAP) kinase, JNK / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2,6-DIHYDROANTHRA/1,9-CD/PYRAZOL-6-ONE / Mitogen-activated protein kinase 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.5 Å
AuthorsScapin, G. / Patel, S.B. / Lisnock, J. / Becker, J.W. / LoGrasso, P.V.
CitationJournal: Chem.Biol. / Year: 2003
Title: The structure of JNK3 in complex with small molecule inhibitors: structural basis for potency and selectivity
Authors: Scapin, G. / Patel, S.B. / Lisnock, J. / Becker, J.W. / LoGrasso, P.V.
History
DepositionJun 11, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)42,2222
Polymers42,0021
Non-polymers2201
Water1,802100
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.207, 73.086, 106.044
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 42001.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MK10_HUMAN / Plasmid: pET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P53779, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Chemical ChemComp-537 / 2,6-DIHYDROANTHRA/1,9-CD/PYRAZOL-6-ONE


Mass: 220.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H8N2O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.22 Å3/Da / Density % sol: 44.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: PEG MMe 550, Ethylene glycol, Hepes, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mg/mlprotein1drop
21 mMAMP-PCP1drop
32 mM1dropMgCl2
420 %PEG550 MME1reservoir
510 %ethylene glycol1reservoir
60.1 MHEPES1reservoirpH7.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 21, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 13541 / Num. obs: 12783 / % possible obs: 94.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 54.9 Å2 / Rsym value: 0.072 / Net I/σ(I): 7
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 1.4 / Num. unique all: 1327 / Rsym value: 0.341 / % possible all: 81.8
Reflection
*PLUS
Redundancy: 5.5 % / Rmerge(I) obs: 0.072
Reflection shell
*PLUS
% possible obs: 81.1 % / Redundancy: 5.8 % / Num. unique obs: 1086 / Rmerge(I) obs: 0.341

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNXrefinement
HKL-2000data reduction
CNXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1PMN

1pmn


Resolution: 2.5→30 Å / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.282 654 5 %random
Rwork0.218 ---
obs0.222 12750 94.3 %-
all-13521 --
Solvent computationSolvent model: Mask / Bsol: 40.3 Å2 / ksol: 0.316 e/Å3
Displacement parametersBiso mean: 51.9 Å2
Baniso -1Baniso -2Baniso -3
1--19.3 Å20 Å20 Å2
2--7.8 Å20 Å2
3---11.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2782 0 17 100 2899
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.24
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_improper_angle_d0.96
X-RAY DIFFRACTIONc_mcbond_it1.61.5
X-RAY DIFFRACTIONc_scbond_it2.62
X-RAY DIFFRACTIONc_mcangle_it2.72
X-RAY DIFFRACTIONc_scangle_it3.72.5
LS refinement shellResolution: 2.5→2.6 Å
RfactorNum. reflection% reflection
Rfree0.366 58 5 %
Rwork0.292 998 -
obs-1056 79.9 %
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.96

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