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- PDB-4u79: Crystal structure of human JNK3 in complex with a benzenesulfonam... -

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Basic information

Entry
Database: PDB / ID: 4u79
TitleCrystal structure of human JNK3 in complex with a benzenesulfonamide inhibitor.
ComponentsMitogen-activated protein kinase 10
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Transferase / TRANSFERASE-TRANSFERASE INHIBITOR complex
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
Chem-3EL / Mitogen-activated protein kinase 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsMohr, C.
CitationJournal: Acs Med.Chem.Lett. / Year: 2015
Title: Unfolded Protein Response in Cancer: IRE1 alpha Inhibition by Selective Kinase Ligands Does Not Impair Tumor Cell Viability.
Authors: Harrington, P.E. / Biswas, K. / Malwitz, D. / Tasker, A.S. / Mohr, C. / Andrews, K.L. / Dellamaggiore, K. / Kendall, R. / Beckmann, H. / Jaeckel, P. / Materna-Reichelt, S. / Allen, J.R. / Lipford, J.R.
History
DepositionJul 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 28, 2015Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / refine_hist / struct_keywords
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.number_atoms_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_keywords.text

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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)42,6262
Polymers42,0601
Non-polymers5671
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.933, 71.632, 106.595
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 / 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: 42059.676 Da / Num. of mol.: 1 / Fragment: UNP residues 39-402
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-3EL / N-{4-[(3-{2-[(trans-4-aminocyclohexyl)amino]pyrimidin-4-yl}pyridin-2-yl)oxy]naphthalen-1-yl}benzenesulfonamide


Mass: 566.673 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H30N6O3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES, 20mMBMe, 30%PEG550MME, pH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 30, 2011
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.23→50 Å / Num. obs: 21261 / % possible obs: 99.9 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.127 / Net I/σ(I): 12.18
Reflection shellResolution: 2.23→2.3 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.558 / Mean I/σ(I) obs: 2.04 / % possible all: 99.9

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Processing

SoftwareName: REFMAC / Version: 5.8.0071 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DA6

3da6


Resolution: 2.23→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.94 / SU B: 19.089 / SU ML: 0.214 / Cross valid method: THROUGHOUT / ESU R: 0.278 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24889 1083 5.1 %RANDOM
Rwork0.21587 ---
obs0.21752 19983 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.958 Å2
Baniso -1Baniso -2Baniso -3
1-4.85 Å20 Å20 Å2
2---1.48 Å20 Å2
3----3.36 Å2
Refinement stepCycle: 1 / Resolution: 2.23→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2737 0 41 33 2811
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192842
X-RAY DIFFRACTIONr_bond_other_d0.0010.022755
X-RAY DIFFRACTIONr_angle_refined_deg1.4181.9863846
X-RAY DIFFRACTIONr_angle_other_deg0.8023.0026309
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3245333
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.99224.275131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.99915513
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5061517
X-RAY DIFFRACTIONr_chiral_restr0.0840.2423
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213132
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02628
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4263.8071344
X-RAY DIFFRACTIONr_mcbond_other2.4263.8061343
X-RAY DIFFRACTIONr_mcangle_it3.8385.6871673
X-RAY DIFFRACTIONr_mcangle_other3.8375.6881674
X-RAY DIFFRACTIONr_scbond_it2.8134.1721498
X-RAY DIFFRACTIONr_scbond_other2.8124.1761499
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5666.132173
X-RAY DIFFRACTIONr_long_range_B_refined6.90630.1743180
X-RAY DIFFRACTIONr_long_range_B_other6.88130.0173169
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.23→2.284 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.441 78 -
Rwork0.414 1366 -
obs--94.5 %
Refinement TLS params.Method: refined / Origin x: -9.8153 Å / Origin y: 20.2102 Å / Origin z: -22.6913 Å
111213212223313233
T0.2175 Å20.0166 Å2-0.0125 Å2-0.0052 Å2-0.014 Å2--0.047 Å2
L0.112 °20.0039 °2-0.2725 °2-1.4555 °20.0608 °2--2.7819 °2
S0.0348 Å °0.0208 Å °-0.0525 Å °0.0554 Å °-0.0213 Å °0.1269 Å °0.0934 Å °-0.0122 Å °-0.0135 Å °

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