+Open data
-Basic information
Entry | Database: PDB / ID: 3o0g | ||||||
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Title | Crystal Structure of Cdk5:p25 in complex with an ATP analogue | ||||||
Components |
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Keywords | TRANSFERASE/TRANSFERASE ACTIVATOR / kinase / Kinase activator complex / kinase inhibitor complex / TRANSFERASE-TRANSFERASE ACTIVATOR complex | ||||||
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 / negative regulation of cell cycle / alpha-tubulin binding / 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 / protein serine/threonine kinase activator activity / axonogenesis / cerebellum development / 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 / molecular replacement / Resolution: 1.95 Å | ||||||
Authors | Mapelli, M. | ||||||
Citation | Journal: Chem.Biol. / Year: 2005 Title: Defining Cdk5 ligand chemical space with small molecule inhibitors of Tau phosphorylation Authors: Ahn, J.S. / Radhakrishnan, M.L. / Mapelli, M. / Choi, S. / Tidor, B. / Cuny, G.D. / Musacchio, A. / Yeh, L. / Kosik, S.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3o0g.cif.gz | 354.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3o0g.ent.gz | 291.9 KB | Display | PDB format |
PDBx/mmJSON format | 3o0g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o0/3o0g ftp://data.pdbj.org/pub/pdb/validation_reports/o0/3o0g | HTTPS FTP |
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-Related structure data
Related structure data | 1h4lS 3o0s S: Starting model for refinement |
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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 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: Cdk5 / Cell line (production host): sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q00535, cyclin-dependent kinase #2: Protein | Mass: 17216.852 Da / Num. of mol.: 2 / Fragment: UNP residues 146-293 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: p25 / Cell line (production host): sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q15078 #3: Chemical | ChemComp-3O0 / { | #4: Water | ChemComp-HOH / | |
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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: 3.05 Å3/Da / Density % sol: 59.66 % |
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Crystal grow | Temperature: 293 K / pH: 7 Details: PEG 3350, KI, Bis-Tris Propane, pH 7, vapor diffusion, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 15, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→25 Å / Num. obs: 88794 / % possible obs: 98.6 % / Rsym value: 0.04 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 1.95→2 Å / Mean I/σ(I) obs: 1.8 / Rsym value: 0.29 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1H4L Resolution: 1.95→19.96 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.916 / Occupancy max: 1 / Occupancy min: 1 / SU B: 3.598 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 24.947 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→19.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.951→2.001 Å / Total num. of bins used: 20 /
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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