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Yorodumi- PDB-8c5j: Spatial structure of Lch-alpha peptide from two-component lantibi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8c5j | ||||||||||||
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Title | Spatial structure of Lch-alpha peptide from two-component lantibiotic system Lichenicidin VK21 | ||||||||||||
Components | Lantibiotic lichenicidin VK21 A1 | ||||||||||||
Keywords | ANTIBIOTIC / LICHENICIDIN VK21 / LANTIBIOTICS / LCHA / LANTHIONINE / THIOESTER / TWO-COMPONENT LANTIBIOTIC SYSTEM | ||||||||||||
Function / homology | Lantibiotic alpha component / Lantibiotic alpha / cytolysis / defense response to Gram-positive bacterium / signaling receptor binding / extracellular space / Lantibiotic lichenicidin VK21 A1 Function and homology information | ||||||||||||
Biological species | Bacillus licheniformis (bacteria) | ||||||||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||||||||
Authors | Mineev, K.S. / Paramonov, A.S. / Arseniev, A.S. / Ovchinnikova, T.V. / Shenkarev, Z.O. | ||||||||||||
Funding support | Russian Federation, 1items
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Citation | Journal: Int J Mol Sci / Year: 2023 Title: Specific Binding of the alpha-Component of the Lantibiotic Lichenicidin to the Peptidoglycan Precursor Lipid II Predetermines Its Antimicrobial Activity. Authors: Panina, I.S. / Balandin, S.V. / Tsarev, A.V. / Chugunov, A.O. / Tagaev, A.A. / Finkina, E.I. / Antoshina, D.V. / Sheremeteva, E.V. / Paramonov, A.S. / Rickmeyer, J. / Bierbaum, G. / Efremov, ...Authors: Panina, I.S. / Balandin, S.V. / Tsarev, A.V. / Chugunov, A.O. / Tagaev, A.A. / Finkina, E.I. / Antoshina, D.V. / Sheremeteva, E.V. / Paramonov, A.S. / Rickmeyer, J. / Bierbaum, G. / Efremov, R.G. / Shenkarev, Z.O. / Ovchinnikova, T.V. #1: Journal: Biochemistry / Year: 2010 Title: Isolation, structure elucidation, and synergistic antibacterial activity of a novel two-component lantibiotic lichenicidin from Bacillus licheniformis VK21. Authors: Shenkarev, Z.O. / Finkina, E.I. / Nurmukhamedova, E.K. / Balandin, S.V. / Mineev, K.S. / Nadezhdin, K.D. / Yakimenko, Z.A. / Tagaev, A.A. / Temirov, Y.V. / Arseniev, A.S. / Ovchinnikova, T.V. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8c5j.cif.gz | 188.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8c5j.ent.gz | 153.5 KB | Display | PDB format |
PDBx/mmJSON format | 8c5j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c5/8c5j ftp://data.pdbj.org/pub/pdb/validation_reports/c5/8c5j | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data | Similarity search - Function & homologyF&H Search |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 3261.921 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: LICHENICIDIN VK21 IS A TETRACYCLIC PEPTIDE. THIOETHER BONDS WITH CYSTEINE RESULT IN FOUR RINGS CROSSLINK 3-7 BETA-METHYLLANTHIONINE (DBB-CYS) CROSSLINK 11-21 LANTHIONINE (DAL-CYS) CROSSLINK ...Details: LICHENICIDIN VK21 IS A TETRACYCLIC PEPTIDE. THIOETHER BONDS WITH CYSTEINE RESULT IN FOUR RINGS CROSSLINK 3-7 BETA-METHYLLANTHIONINE (DBB-CYS) CROSSLINK 11-21 LANTHIONINE (DAL-CYS) CROSSLINK 22-27 BETA-METHYLLANTHIONINE (DBB-CYS) CROSSLINK 24-31 BETA-METHYLLANTHIONINE (DBB-CYS Source: (natural) Bacillus licheniformis (bacteria) / Strain: VK21 / References: UniProt: P86475 |
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Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution / Contents: 0.5 mM LCHA-1, methanol / Label: lhcdA / Solvent system: methanol |
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Sample | Conc.: 0.5 mM / Component: LCHA-1 / Isotopic labeling: natural abundance |
Sample conditions | Ionic strength: 0 mM / Ionic strength err: 0 / Label: cond_1 / pH: 3.5 / PH err: 0.1 / Pressure: AMBIENT bar / Pressure err: 0.01 / Temperature: 300 K / Temperature err: 0.1 |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 | ||||||||||||||||||||||||
NMR representative | Selection criteria: target function | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 400 / Conformers submitted total number: 20 |