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- PDB-1pmu: The crystal structure of JNK3 in complex with a phenantroline inh... -

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Basic information

Entry
Database: PDB / ID: 1pmu
TitleThe crystal structure of JNK3 in complex with a phenantroline 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 / cytosol / cytoplasm
Similarity search - Function
Mitogen-activated protein (MAP) kinase, JNK / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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. / : / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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
9-(4-HYDROXYPHENYL)-2,7-PHENANTHROLINE / Mitogen-activated protein kinase 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 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)42,3093
Polymers42,0021
Non-polymers3082
Water1,13563
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.401, 62.377, 98.119
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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-9HP / 9-(4-HYDROXYPHENYL)-2,7-PHENANTHROLINE


Mass: 272.301 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H12N2O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.27 Å3/Da / Density % sol: 45.87 %
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: Aug 4, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→25 Å / Num. all: 10987 / Num. obs: 10987 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 55.8 Å2 / Rsym value: 0.123 / Net I/σ(I): 5.7
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 1.3 / Num. unique all: 1668 / Rsym value: 0.454 / % possible all: 100
Reflection
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.123
Reflection shell
*PLUS
% possible obs: 100 % / Num. unique obs: 1668 / Rmerge(I) obs: 0.454

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Processing

Software
NameClassification
X-GENdata scaling
X-GENdata reduction
CNXrefinement
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PMN

1pmn


Resolution: 2.7→25 Å / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.285 541 5 %random
Rwork0.218 ---
obs0.221 10946 95.5 %-
all-10989 --
Solvent computationSolvent model: Mask / Bsol: 15.9 Å2 / ksol: 0.331 e/Å3
Displacement parametersBiso mean: 31.4 Å2
Baniso -1Baniso -2Baniso -3
1-2.5 Å20 Å20 Å2
2--5.7 Å20 Å2
3----8.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.7→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2749 0 22 63 2834
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.42
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_improper_angle_d0.983
X-RAY DIFFRACTIONc_mcbond_it1.61.5
X-RAY DIFFRACTIONc_scbond_it2.62
X-RAY DIFFRACTIONc_mcangle_it2.42
X-RAY DIFFRACTIONc_scangle_it3.42.5
LS refinement shellResolution: 2.7→2.8 Å
RfactorNum. reflection% reflection
Rfree0.389 43 5 %
Rwork0.347 914 -
obs-957 88.7 %
Refinement
*PLUS
Num. reflection obs: 10496
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.983

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