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Yorodumi- PDB-6bjn: PICK1 PDZ domain in complex with the class I PDZ binding motif QSAV -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bjn | ||||||
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Title | PICK1 PDZ domain in complex with the class I PDZ binding motif QSAV | ||||||
Components | PRKCA-binding protein | ||||||
Keywords | PEPTIDE BINDING PROTEIN / PICK1 PDZ Domain Class II PDZ binding motif | ||||||
Function / homology | Function and homology information membrane curvature sensor activity / postsynaptic early endosome / glial cell development / neuronal ion channel clustering / cellular response to decreased oxygen levels / Arp2/3 complex binding / Trafficking of GluR2-containing AMPA receptors / epigenetic programming of gene expression / regulation of Arp2/3 complex-mediated actin nucleation / negative regulation of Arp2/3 complex-mediated actin nucleation ...membrane curvature sensor activity / postsynaptic early endosome / glial cell development / neuronal ion channel clustering / cellular response to decreased oxygen levels / Arp2/3 complex binding / Trafficking of GluR2-containing AMPA receptors / epigenetic programming of gene expression / regulation of Arp2/3 complex-mediated actin nucleation / negative regulation of Arp2/3 complex-mediated actin nucleation / monoamine transport / genomic imprinting / protein kinase C-activating G protein-coupled receptor signaling pathway / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / dendritic spine organization / long-term synaptic depression / dendritic spine maintenance / receptor clustering / regulation of insulin secretion / positive regulation of receptor internalization / cellular response to glucose starvation / protein kinase C binding / trans-Golgi network membrane / G protein-coupled receptor binding / Cell surface interactions at the vascular wall / phospholipid binding / intracellular protein transport / endocytic vesicle membrane / actin filament binding / synaptic vesicle / presynaptic membrane / postsynaptic density / cytoskeleton / neuron projection / protein domain specific binding / signaling receptor binding / protein phosphorylation / synapse / perinuclear region of cytoplasm / Golgi apparatus / identical protein binding / metal ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.43 Å | ||||||
Authors | Marcotte, D.J. | ||||||
Citation | Journal: Protein Sci. / Year: 2018 Title: Lock and chop: A novel method for the generation of a PICK1 PDZ domain and piperidine-based inhibitor co-crystal structure. Authors: Marcotte, D.J. / Hus, J.C. / Banos, C.C. / Wildes, C. / Arduini, R. / Bergeron, C. / Hession, C.A. / Baker, D.P. / Lin, E. / Guckian, K.M. / Dunah, A.W. / Silvian, L.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6bjn.cif.gz | 45 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bjn.ent.gz | 33.5 KB | Display | PDB format |
PDBx/mmJSON format | 6bjn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bj/6bjn ftp://data.pdbj.org/pub/pdb/validation_reports/bj/6bjn | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 13540.405 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PICK1, PRKCABP / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NRD5 #2: 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: 2.47 Å3/Da / Density % sol: 50.22 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1M BisTRIS pH 5.5 and 25% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 13, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.43→50 Å / Num. obs: 9544 / % possible obs: 99.6 % / Redundancy: 4.8 % / CC1/2: 0.86 / Net I/σ(I): 7.1 |
-Processing
Software |
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Refinement | Resolution: 2.43→47.18 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.927 / SU B: 6.691 / SU ML: 0.157 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.307 / ESU R Free: 0.215
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 94.96 Å2 / Biso mean: 38.799 Å2 / Biso min: 20.86 Å2
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Refinement step | Cycle: final / Resolution: 2.43→47.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.434→2.498 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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