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Yorodumi- PDB-1ung: Structural mechanism for the inhibition of CDK5-p25 by roscovitin... -
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-Basic information
Entry | Database: PDB / ID: 1ung | ||||||
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Title | Structural mechanism for the inhibition of CDK5-p25 by roscovitine, aloisine and indirubin. | ||||||
Components |
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Keywords | CELL CYCLE / COMPLEX(KINASE-ACTIVATOR) / INHIBITORS / 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 / positive regulation of calcium ion-dependent exocytosis / neuron cell-cell adhesion / Activated NTRK2 signals through CDK5 ...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 / positive regulation of calcium ion-dependent exocytosis / neuron cell-cell adhesion / Activated NTRK2 signals through CDK5 / layer formation in cerebral cortex / negative regulation of axon extension / protein localization to synapse / receptor catabolic process / regulation of synaptic vesicle cycle / 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 / axon extension / negative regulation of protein export from nucleus / calcium ion import / cyclin-dependent protein serine/threonine kinase activator activity / motor neuron axon guidance / regulation of synaptic vesicle recycling / axonal fasciculation / cyclin-dependent protein serine/threonine kinase activity / embryo development ending in birth or egg hatching / dendrite morphogenesis / regulation of neuron differentiation / synaptic vesicle transport / tau-protein kinase activity / regulation of cyclin-dependent protein serine/threonine kinase activity / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / protein kinase activator activity / receptor clustering / beta-tubulin binding / oligodendrocyte differentiation / central nervous system neuron development / cyclin-dependent protein kinase holoenzyme complex / synaptic vesicle exocytosis / behavioral response to cocaine / synaptic vesicle endocytosis / negative regulation of cell cycle / DARPP-32 events / alpha-tubulin binding / positive regulation of protein targeting to membrane / ephrin receptor signaling pathway / regulation of protein localization to plasma membrane / regulation of macroautophagy / Schwann cell development / skeletal muscle tissue development / negative regulation of protein ubiquitination / regulation of synaptic transmission, glutamatergic / positive regulation of microtubule polymerization / sensory perception of pain / synapse assembly / NPAS4 regulates expression of target genes / ionotropic glutamate receptor binding / ephrin receptor binding / regulation of cell migration / ionotropic glutamate receptor signaling pathway / phosphorylation / protein serine/threonine kinase activator activity / cerebellum development / cell-matrix adhesion / axonogenesis / excitatory postsynaptic potential / filopodium / synaptic transmission, glutamatergic / axon guidance / hippocampus development / negative regulation of proteolysis / regulation of actin cytoskeleton organization / peptidyl-threonine phosphorylation / intracellular protein transport / neuron migration / Hsp90 protein binding / visual learning / tau protein binding / brain development / neuromuscular junction / regulation of synaptic plasticity / G protein-coupled acetylcholine receptor signaling pathway / neuron differentiation / p53 binding / microtubule cytoskeleton organization / actin filament binding / cellular response to amyloid-beta / rhythmic process / cell junction / positive regulation of neuron apoptotic process / neuron projection development / Factors involved in megakaryocyte development and platelet production / lamellipodium / presynapse / kinase activity Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 | 1ung.cif.gz | 188.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ung.ent.gz | 150.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ung.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ung_validation.pdf.gz | 997.8 KB | Display | wwPDB validaton report |
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Full document | 1ung_full_validation.pdf.gz | 965.5 KB | Display | |
Data in XML | 1ung_validation.xml.gz | 38.5 KB | Display | |
Data in CIF | 1ung_validation.cif.gz | 53.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/un/1ung ftp://data.pdbj.org/pub/pdb/validation_reports/un/1ung | HTTPS FTP |
-Related structure data
Related structure data | 1unhC 1unlC 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: PFASTBAC / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q00535, cyclin-dependent kinase #2: Protein | Mass: 23200.678 Da / Num. of mol.: 2 / Fragment: RESIDUES 100-307 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFASTBAC / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q15078 #3: Chemical | #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: 56.4 % |
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Crystal grow | pH: 7 Details: 13% PEG 3350, 0.1M KI, 0.1M BISTRISPROPANE PH 7.0, 10MM 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: 2.3→25 Å / Num. obs: 53731 / % possible obs: 95.4 % / Observed criterion σ(I): 2.5 / Redundancy: 6.2 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 2.3→2.4 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.6 / % possible all: 97.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1H4L Resolution: 2.3→19.76 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.921 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.293 / ESU R Free: 0.201 / 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: 22.42 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→19.76 Å
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