- PDB-8ym2: Crystal structure of AIDA-1 PTB domain in complex with SynGAP NPx... -
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Basic information
Entry
Database: PDB / ID: 8ym2
Title
Crystal structure of AIDA-1 PTB domain in complex with SynGAP NPxF motif
Components
Ankyrin repeat and sterile alpha motif domain-containing protein 1B
Ras/Rap GTPase-activating protein SynGAP
Keywords
PROTEIN BINDING / AIDA-1 / ANKS1B / SynGAP / Ras and Rab interactor / PTB domain
Function / homology
Function and homology information
Regulation of RAS by GAPs / negative regulation of axonogenesis / pattern specification process / maintenance of postsynaptic specialization structure / negative regulation of Ras protein signal transduction / regulation of synapse structure or activity / dendrite development / receptor clustering / regulation of MAPK cascade / postsynaptic density, intracellular component ...Regulation of RAS by GAPs / negative regulation of axonogenesis / pattern specification process / maintenance of postsynaptic specialization structure / negative regulation of Ras protein signal transduction / regulation of synapse structure or activity / dendrite development / receptor clustering / regulation of MAPK cascade / postsynaptic density, intracellular component / axonogenesis / GTPase activator activity / dendritic shaft / regulation of long-term neuronal synaptic plasticity / visual learning / modulation of chemical synaptic transmission / regulation of synaptic plasticity / SH3 domain binding / neuron apoptotic process / negative regulation of neuron apoptotic process / Ras protein signal transduction / postsynaptic density / glutamatergic synapse / synapse / protein kinase binding / membrane / plasma membrane / cytoplasm Similarity search - Function
Disabled homolog 2-interacting protein, C-terminal domain / SynGAP, PH domain / Disabled homolog 2-interacting protein, C-terminal domain / Ankyrin repeat and SAM domain-containing protein 1, SAM repeat 1 / Ankyrin repeat and SAM domain-containing protein 1, SAM repeat 2 / : / Ras GTPase-activating protein / Ras GTPase-activating protein, conserved site / Ras GTPase-activating proteins domain signature. / GTPase-activator protein for Ras-like GTPase ...Disabled homolog 2-interacting protein, C-terminal domain / SynGAP, PH domain / Disabled homolog 2-interacting protein, C-terminal domain / Ankyrin repeat and SAM domain-containing protein 1, SAM repeat 1 / Ankyrin repeat and SAM domain-containing protein 1, SAM repeat 2 / : / Ras GTPase-activating protein / Ras GTPase-activating protein, conserved site / Ras GTPase-activating proteins domain signature. / GTPase-activator protein for Ras-like GTPase / Ras GTPase-activating proteins profile. / GTPase-activator protein for Ras-like GTPases / Ras GTPase-activating domain / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / SAM domain (Sterile alpha motif) / Rho GTPase activation protein / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / C2 domain superfamily / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily Similarity search - Domain/homology
Ankyrin repeat and sterile alpha motif domain-containing protein 1B / Ras/Rap GTPase-activating protein SynGAP Similarity search - Component
Resolution: 2→25.26 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.198 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.26378
750
4.7 %
RANDOM
Rwork
0.21311
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obs
0.21551
15191
97.84 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK