[English] 日本語
Yorodumi- PDB-5zyx: Solution NMR structure of K30 peptide in 10 mM dioctanoyl phospha... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zyx | ||||||
---|---|---|---|---|---|---|---|
Title | Solution NMR structure of K30 peptide in 10 mM dioctanoyl phosphatidylglycerol (D8PG) | ||||||
Components | ARG-TRP-LYS-ARG-HIS-ILE-SER-GLU-GLN-LEU-ARG-ARG-ARG-ASP-ARG-LEU-GLN-ARG-GLN-ALA | ||||||
Keywords | ANTIMICROBIAL PROTEIN / STRUCTURE FROM CYANA 2.1 / K30 / D8PG | ||||||
Function / homology | Function and homology information Atg12-Atg5-Atg16 complex / C-terminal protein lipidation / vacuole-isolation membrane contact site / ubiquitin-like protein transferase activity / microautophagy / xenophagy / protein localization to phagophore assembly site / phagophore assembly site membrane / corpus callosum development / negative stranded viral RNA replication ...Atg12-Atg5-Atg16 complex / C-terminal protein lipidation / vacuole-isolation membrane contact site / ubiquitin-like protein transferase activity / microautophagy / xenophagy / protein localization to phagophore assembly site / phagophore assembly site membrane / corpus callosum development / negative stranded viral RNA replication / endolysosome membrane / Macroautophagy / axoneme / autophagosome membrane / autophagosome assembly / autophagosome / positive regulation of autophagy / protein-membrane adaptor activity / sperm midpiece / hippocampus development / macroautophagy / protein transport / GTPase binding / defense response to virus / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Bhunia, A. / Mohid, A. / Stella, L. / Calligari, P. | ||||||
Funding support | India, 1items
| ||||||
Citation | Journal: Bioconjug.Chem. / Year: 2019 Title: Design, Synthesis, Antibacterial Potential, and Structural Characterization of N-Acylated Derivatives of the Human Autophagy 16 Polypeptide. Authors: Varnava, K.G. / Mohid, S.A. / Calligari, P. / Stella, L. / Reynison, J. / Bhunia, A. / Sarojini, V. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5zyx.cif.gz | 172.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5zyx.ent.gz | 122.6 KB | Display | PDB format |
PDBx/mmJSON format | 5zyx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zy/5zyx ftp://data.pdbj.org/pub/pdb/validation_reports/zy/5zyx | HTTPS FTP |
---|
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
---|---|
Other databases |
|
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein/peptide | Mass: 2698.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q676U5*PLUS |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-Sample preparation
Details | Type: solution / Contents: 1 mM 1H K30 Peptide, 90% H2O/10% D2O / Label: 1H / Solvent system: 90% H2O/10% D2O |
---|---|
Sample | Conc.: 1 mM / Component: K30 Peptide / Isotopic labeling: 1H |
Sample conditions | Ionic strength: 0 Not defined / Label: Solution in water / pH: 4.5 / Pressure: 1 bar / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 500 MHz |
---|
-Processing
NMR software |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: simulated annealing / Software ordinal: 3 | |||||||||||||||
NMR representative | Selection criteria: lowest energy | |||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |