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Yorodumi- PDB-1p5k: HP (2-20) Substitution SER to LEU11 modification in sds-d25 micelles -
+Open data
-Basic information
Entry | Database: PDB / ID: 1p5k | ||||||
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Title | HP (2-20) Substitution SER to LEU11 modification in sds-d25 micelles | ||||||
Components | 19-mer peptide from 50S ribosomal protein L1 | ||||||
Keywords | RIBOSOME / COIL-HELIX-COIL | ||||||
Function / homology | Function and homology information regulation of translation / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / defense response to bacterium / translation Similarity search - Function | ||||||
Method | SOLUTION NMR / HYBRID DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING | ||||||
Authors | Lee, K.H. / Lee, D.G. / Park, Y.K. / Harm, K.S. / Kim, Y.M. | ||||||
Citation | Journal: To be published Title: Interactions between antimicrobial peptide, HP(2-20) derived from helicobacter pylori, and membrain studied by nmr spectroscopy Authors: Lee, K.H. / Lee, D.G. / Park, Y.K. / Harm, K.S. / Kim, Y.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1p5k.cif.gz | 121.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1p5k.ent.gz | 95.6 KB | Display | PDB format |
PDBx/mmJSON format | 1p5k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1p5k_validation.pdf.gz | 338 KB | Display | wwPDB validaton report |
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Full document | 1p5k_full_validation.pdf.gz | 416.4 KB | Display | |
Data in XML | 1p5k_validation.xml.gz | 6.7 KB | Display | |
Data in CIF | 1p5k_validation.cif.gz | 10.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p5/1p5k ftp://data.pdbj.org/pub/pdb/validation_reports/p5/1p5k | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 2299.756 Da / Num. of mol.: 1 / Mutation: L11S / Source method: obtained synthetically Details: this peptide was chemically synthesized. The sequence for this peptide which N-terminus of Helicobacter pylori ribosomal protein L1 References: UniProt: Q9ZK21, UniProt: P56029*PLUS |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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NMR details | Text: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR TECHNIQUES |
-Sample preparation
Details | Contents: 1.5MM PEPTIDE; 150MM SDS-D25 / Solvent system: 90% H2O/10% D2O |
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Sample conditions | pH: 6 / Pressure: 1 atm / Temperature: 318 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 400 MHz |
-Processing
NMR software |
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Refinement | Method: HYBRID DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING Software ordinal: 1 | ||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 50 / Conformers submitted total number: 20 |