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- PDB-1pmn: Crystal structure of JNK3 in complex with an imidazole-pyrimidine... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1pmn | ||||||
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Title | Crystal structure of JNK3 in complex with an imidazole-pyrimidine inhibitor | ||||||
![]() | Mitogen-activated protein kinase 10 | ||||||
![]() | TRANSFERASE / MAP kinase / apoptosis / inhibition | ||||||
Function / homology | ![]() 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 / regulation of circadian rhythm / FCERI mediated MAPK activation ...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 / regulation of circadian rhythm / FCERI mediated MAPK activation / 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 | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Scapin, G. / Patel, S.B. / Lisnock, J. / Becker, J.W. / LoGrasso, P.V. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 88.7 KB | Display | ![]() |
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PDB format | ![]() | 64.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1pmuC ![]() 1pmvC ![]() 4z9lC ![]() 1jnkS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 42001.641 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P53779, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor |
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#2: Chemical | ChemComp-984 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 49.05 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG MMe 550, Ethylene glycol, Hepes, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.3 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 6, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→22 Å / Num. all: 21324 / Num. obs: 21026 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 30.9 Å2 / Rsym value: 0.059 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 3483 / Rsym value: 0.197 / % possible all: 98.5 |
Reflection | *PLUS Rmerge(I) obs: 0.059 |
Reflection shell | *PLUS % possible obs: 98.5 % / Num. unique obs: 3431 / Rmerge(I) obs: 0.197 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1JNK Resolution: 2.2→22 Å / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: Mask / Bsol: 52.9 Å2 / ksol: 0.396 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.28 Å
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Refine LS restraints | *PLUS
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