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- 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. | ||||||
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![]() | CYCLIN DEPENDENT KINASE / INHIBITOR / ATP-ANALOGUE / NEURODEGENERATIVE DISEASES | ||||||
Function / homology | ![]() 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 / neuron cell-cell adhesion ...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 / neuron cell-cell adhesion / positive regulation of calcium ion-dependent exocytosis / 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 / cyclin-dependent protein serine/threonine kinase activator activity / regulation of synaptic vesicle recycling / axonal fasciculation / motor neuron axon guidance / dendrite morphogenesis / embryo development ending in birth or egg hatching / regulation of neuron differentiation / synaptic vesicle transport / regulation of cyclin-dependent protein serine/threonine kinase activity / tau-protein kinase activity / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / beta-tubulin binding / protein kinase activator activity / central nervous system neuron development / oligodendrocyte differentiation / receptor clustering / synaptic vesicle exocytosis / behavioral response to cocaine / synaptic vesicle endocytosis / negative regulation of cell cycle / DARPP-32 events / alpha-tubulin binding / cyclin-dependent protein kinase holoenzyme complex / positive regulation of protein targeting to membrane / ephrin receptor signaling pathway / regulation of protein localization to plasma membrane / regulation of macroautophagy / cyclin-dependent protein serine/threonine kinase activity / Schwann cell development / skeletal muscle tissue development / regulation of synaptic transmission, glutamatergic / regulation of cell migration / sensory perception of pain / positive regulation of microtubule polymerization / negative regulation of protein ubiquitination / synapse assembly / NPAS4 regulates expression of target genes / ionotropic glutamate receptor signaling pathway / excitatory postsynaptic potential / ephrin receptor binding / protein serine/threonine kinase activator activity / cerebellum development / axonogenesis / cell-matrix adhesion / filopodium / synaptic transmission, glutamatergic / hippocampus development / negative regulation of proteolysis / regulation of actin cytoskeleton organization / peptidyl-threonine phosphorylation / axon guidance / intracellular protein transport / ionotropic glutamate receptor binding / neuron migration / Hsp90 protein binding / visual learning / regulation of synaptic plasticity / tau protein binding / neuromuscular junction / neuron differentiation / G protein-coupled acetylcholine receptor signaling pathway / brain development / microtubule cytoskeleton organization / cellular response to amyloid-beta / neuron projection development / actin filament binding / positive regulation of neuron apoptotic process / rhythmic process / p53 binding / presynapse / lamellipodium / cell junction / kinase activity / Factors involved in megakaryocyte development and platelet production / growth cone Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mapelli, M. / Crovace, C. / Massimiliano, L. / Musacchio, A. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 191 KB | Display | ![]() |
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PDB format | ![]() | 151.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 812.1 KB | Display | ![]() |
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Full document | ![]() | 837.7 KB | Display | |
Data in XML | ![]() | 36.7 KB | Display | |
Data in CIF | ![]() | 51.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ungC ![]() 1unhC ![]() 1h4lS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() 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.) ![]() ![]() ![]() #3: Chemical | ChemComp-RRC / | #4: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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