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Yorodumi- PDB-2g9p: NMR structure of a novel antimicrobial peptide, latarcin 2a, from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2g9p | ||||||
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Title | NMR structure of a novel antimicrobial peptide, latarcin 2a, from spider (Lachesana tarabaevi) venom | ||||||
Components | antimicrobial peptide Latarcin 2a | ||||||
Keywords | ANTIMICROBIAL PROTEIN / helix-hinge-helix | ||||||
Function / homology | Latarcin precursor / Latarcin precursor / hemolysis in another organism / defense response to fungus / toxin activity / defense response to bacterium / extracellular region / M-zodatoxin-Lt2a Function and homology information | ||||||
Method | SOLUTION NMR / torsion angle dynamics, refinement in implicit membrane model (water, octanol, water slab) | ||||||
Authors | Dubovskii, P.V. / Volynsky, P.E. / Polyansky, A.A. / Chupin, V.V. / Efremov, R.G. / Arseniev, A.S. | ||||||
Citation | Journal: Biochemistry / Year: 2006 Title: Spatial structure and activity mechanism of a novel spider antimicrobial peptide. Authors: Dubovskii, P.V. / Volynsky, P.E. / Polyansky, A.A. / Chupin, V.V. / Efremov, R.G. / Arseniev, A.S. | ||||||
History |
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Remark 999 | SEQUENCE The sequence of the protein has not been deposited into any sequence database. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2g9p.cif.gz | 173.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2g9p.ent.gz | 144 KB | Display | PDB format |
PDBx/mmJSON format | 2g9p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2g9p_validation.pdf.gz | 327.1 KB | Display | wwPDB validaton report |
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Full document | 2g9p_full_validation.pdf.gz | 380.8 KB | Display | |
Data in XML | 2g9p_validation.xml.gz | 7.5 KB | Display | |
Data in CIF | 2g9p_validation.cif.gz | 12.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g9/2g9p ftp://data.pdbj.org/pub/pdb/validation_reports/g9/2g9p | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 2912.610 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The peptide was chemically synthesized. The sequence can be naturally found in spider (Lachesana tarabaevi) venom References: UniProt: Q1ELU1 |
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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 |
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Sample conditions |
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-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | |||||||||||||||
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Radiation wavelength | Relative weight: 1 | |||||||||||||||
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics, refinement in implicit membrane model (water, octanol, water slab) Software ordinal: 1 Details: In total, 222 distance and 123 torsion angles constraints were used for structure calculation | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20 |