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- PDB-4z9l: THE STRUCTURE OF JNK3 IN COMPLEX WITH AN IMIDAZOLE-PYRIMIDINE INH... -

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Basic information

Entry
Database: PDB / ID: 4z9l
TitleTHE STRUCTURE OF JNK3 IN COMPLEX WITH AN IMIDAZOLE-PYRIMIDINE INHIBITOR
ComponentsMitogen-activated protein kinase 10
KeywordsTRANSFERASE/INHIBITOR / MAP KINASE / APOPTOSIS / INHIBITION / 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-880 / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Mitogen-activated protein kinase 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsScapin, G. / Patel, S.B. / Lisnock, J. / Becker, J.W. / Lograsso, P.V. / Smart, O.S. / Bricogne, G.
Citation
Journal: 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.
#1: Journal: Multifaceted Roles Of Crystallography In Modern Drug Discovery
Year: 2015
Title: Achieving High Quality Ligand Chemistry in Protein-Ligand Crystal Structures for Drug Design
Authors: Smart, O.S. / Bricogne, G.
History
DepositionApr 10, 2015Deposition site: RCSB / Processing site: RCSB
SupersessionMay 6, 2015ID: 1PMQ
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_validate_close_contact / refine_hist / struct_keywords
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.d_res_high / _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)43,0216
Polymers42,0021
Non-polymers1,0205
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.951, 71.525, 106.000
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: 42001.641 Da / Num. of mol.: 1 / Fragment: UNP residues 40-401
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK10, JNK3, JNK3A, PRKM10, SAPK1B / Plasmid: PET15B / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P53779, mitogen-activated protein kinase
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-880 / CYCLOHEXYL-{4-[5-(3,4-DICHLOROPHENYL)-2-PIPERIDIN-4-YL-3-PROPYL-3H-IMIDAZOL-4-YL]-PYRIMIDIN-2-YL}AMINE


Mass: 513.505 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H34Cl2N6
#4: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 3 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.3 Å3/Da / Density % sol: 46.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG MME 550, ETHYLENE GLYCOL, HEPES

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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 7, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→17 Å / Num. obs: 19586 / % possible obs: 95.6 % / Observed criterion σ(I): -3 / Redundancy: 7.8 % / Biso Wilson estimate: 25.31 Å2 / Rsym value: 0.061 / Net I/σ(I): 10
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 3 / % possible all: 80.1

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
HKL-2000data reduction
SCALEPACKdata scaling
Cootmodel building
CNXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1PMN

1pmn


Resolution: 2.1→16.94 Å / Cor.coef. Fo:Fc: 0.9182 / Cor.coef. Fo:Fc free: 0.8926 / SU R Cruickshank DPI: 0.256 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.256 / SU Rfree Blow DPI: 0.187 / SU Rfree Cruickshank DPI: 0.188
RfactorNum. reflection% reflectionSelection details
Rfree0.2258 957 4.89 %RANDOM
Rwork0.1997 ---
obs0.201 19586 84.31 %-
Displacement parametersBiso mean: 29.49 Å2
Baniso -1Baniso -2Baniso -3
1-7.8069 Å20 Å20 Å2
2---3.0291 Å20 Å2
3----4.7778 Å2
Refine analyzeLuzzati coordinate error obs: 0.294 Å
Refinement stepCycle: LAST / Resolution: 2.1→16.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2636 0 69 67 2772
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012826HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.993889HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d961SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes64HARMONIC2
X-RAY DIFFRACTIONt_gen_planes447HARMONIC5
X-RAY DIFFRACTIONt_it2826HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.23
X-RAY DIFFRACTIONt_other_torsion16.71
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion355SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies1HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3303SEMIHARMONIC4
LS refinement shellResolution: 2.1→2.21 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3129 65 5.5 %
Rwork0.1792 1117 -
all0.187 1182 -
obs--35.39 %
Refinement TLS params.Method: refined / Origin x: 16.464 Å / Origin y: 15.1023 Å / Origin z: 23.1047 Å
111213212223313233
T-0.0929 Å2-0.0159 Å2-0.0011 Å2--0.1595 Å2-0.0099 Å2---0.1329 Å2
L0.48 °2-0.1745 °20.4235 °2-1.5444 °20.4799 °2--4.0401 °2
S0.0236 Å °-0.0045 Å °-0.0112 Å °-0.0301 Å °-0.0509 Å °0.03 Å °-0.0191 Å °-0.1145 Å °0.0272 Å °
Refinement TLS groupSelection details: { A|* }

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