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Yorodumi- PDB-1unl: Structural mechanism for the inhibition of CD5-p25 from the rosco... -
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-Basic information
Entry | Database: PDB / ID: 1unl | ||||||
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Title | Structural mechanism for the inhibition of CD5-p25 from the roscovitine, aloisine and indirubin. | ||||||
Components |
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Keywords | CYCLIN DEPENDENT KINASE / INHIBITOR / ATP-ANALOGUE / NEURODEGENERATIVE DISEASES | ||||||
Function / homology | Function and homology information superior olivary nucleus maturation / protein kinase 5 complex / acetylcholine receptor activator activity / G1 to G0 transition involved in cell differentiation / ErbB-2 class receptor binding / negative regulation of synaptic plasticity / contractile muscle fiber / Activated NTRK2 signals through CDK5 / layer formation in cerebral cortex / positive regulation of calcium ion-dependent exocytosis ...superior olivary nucleus maturation / protein kinase 5 complex / acetylcholine receptor activator activity / G1 to G0 transition involved in cell differentiation / ErbB-2 class receptor binding / negative regulation of synaptic plasticity / contractile muscle fiber / Activated NTRK2 signals through CDK5 / layer formation in cerebral cortex / positive regulation of calcium ion-dependent exocytosis / neuron cell-cell adhesion / negative regulation of axon extension / receptor catabolic process / regulation of synaptic vesicle cycle / protein localization to synapse / corpus callosum development / regulation of dendritic spine morphogenesis / cerebellar cortex formation / CRMPs in Sema3A signaling / NGF-stimulated transcription / synaptic transmission, dopaminergic / ErbB-3 class receptor binding / calcium ion import / negative regulation of protein export from nucleus / axon extension / regulation of synaptic vesicle recycling / motor neuron axon guidance / cyclin-dependent protein serine/threonine kinase activator activity / axonal fasciculation / dendrite morphogenesis / embryo development ending in birth or egg hatching / regulation of neuron differentiation / synaptic vesicle transport / tau-protein kinase activity / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / protein kinase activator activity / beta-tubulin binding / central nervous system neuron development / oligodendrocyte differentiation / receptor clustering / synaptic vesicle exocytosis / regulation of cyclin-dependent protein serine/threonine kinase activity / behavioral response to cocaine / synaptic vesicle endocytosis / alpha-tubulin binding / negative regulation of cell cycle / DARPP-32 events / cyclin-dependent protein kinase holoenzyme complex / positive regulation of protein targeting to membrane / regulation of macroautophagy / ephrin receptor signaling pathway / regulation of protein localization to plasma membrane / cyclin-dependent protein serine/threonine kinase activity / Schwann cell development / skeletal muscle tissue development / positive regulation of microtubule polymerization / regulation of cell migration / regulation of synaptic transmission, glutamatergic / sensory perception of pain / negative regulation of protein ubiquitination / synapse assembly / ionotropic glutamate receptor binding / NPAS4 regulates expression of target genes / ionotropic glutamate receptor signaling pathway / excitatory postsynaptic potential / ephrin receptor binding / cerebellum development / protein serine/threonine kinase activator activity / axonogenesis / cell-matrix adhesion / filopodium / synaptic transmission, glutamatergic / hippocampus development / regulation of actin cytoskeleton organization / negative regulation of proteolysis / axon guidance / peptidyl-threonine phosphorylation / intracellular protein transport / neuron migration / Hsp90 protein binding / regulation of synaptic plasticity / brain development / visual learning / neuromuscular junction / tau protein binding / neuron differentiation / G protein-coupled acetylcholine receptor signaling pathway / microtubule cytoskeleton organization / cellular response to amyloid-beta / neuron projection development / positive regulation of neuron apoptotic process / actin filament binding / rhythmic process / p53 binding / presynapse / cell junction / lamellipodium / kinase activity / Factors involved in megakaryocyte development and platelet production / growth cone Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Mapelli, M. / Crovace, C. / Massimiliano, L. / Musacchio, A. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2005 Title: Mechanism of Cdk5/P25 Binding by Cdk Inhibitors Authors: Mapelli, M. / Massimilinao, L. / Crovace, C. / Seeliger, M.A. / Tsai, L.-H. / Meijer, L. / Musacchio, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1unl.cif.gz | 191 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1unl.ent.gz | 151.6 KB | Display | PDB format |
PDBx/mmJSON format | 1unl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/un/1unl ftp://data.pdbj.org/pub/pdb/validation_reports/un/1unl | HTTPS FTP |
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-Related structure data
Related structure data | 1ungC 1unhC 1h4lS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 33349.477 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PBAC1 / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) References: UniProt: Q00535, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor #2: Protein | Mass: 23200.678 Da / Num. of mol.: 2 / Fragment: RESIDUES 100-307 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PBAC1 / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q15078 #3: Chemical | ChemComp-RRC / | #4: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56 % |
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Crystal grow | pH: 7 Details: 13% PEG 3350, 0.1 M KI, 0.1 M BISTRISPROPANE PH 7.0, 10 MM DTT |
-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 15, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→25 Å / Num. obs: 64818 / % possible obs: 94.6 % / Observed criterion σ(I): 2.5 / Redundancy: 8.8 % / Rmerge(I) obs: 0.011 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 3 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.8 / % possible all: 97.7 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1H4L Resolution: 2.2→19.76 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.935 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.254 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.02 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→19.76 Å
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