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Yorodumi- PDB-1t5m: Structural transitions as determinants of the action of the calci... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1t5m | ||||||
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Title | Structural transitions as determinants of the action of the calcium-dependent antibiotic daptomycin | ||||||
Components | DAPTOMYCIN | ||||||
Keywords | ANTIBIOTIC / DAPTOMYCIN / CUBICIN / LIPOPEPTIDE / CALCIUM-DEPENDENT | ||||||
Function / homology | Daptomycin / DECANOIC ACID / : Function and homology information | ||||||
Biological species | STREPTOMYCES ROSEOSPORUS (bacteria) | ||||||
Method | SOLUTION NMR | ||||||
Authors | Jung, D. / Rozek, A. / Okon, M. / Hancock, R.E. | ||||||
Citation | Journal: Chem.Biol. / Year: 2004 Title: Structural Transitions as Determinants of the Action of the Calcium-Dependent Antibiotic Daptomycin. Authors: Jung, D. / Rozek, A. / Okon, M. / Hancock, R.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1t5m.cif.gz | 63.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1t5m.ent.gz | 49.1 KB | Display | PDB format |
PDBx/mmJSON format | 1t5m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1t5m_validation.pdf.gz | 369.1 KB | Display | wwPDB validaton report |
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Full document | 1t5m_full_validation.pdf.gz | 451.2 KB | Display | |
Data in XML | 1t5m_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | 1t5m_validation.cif.gz | 13.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t5/1t5m ftp://data.pdbj.org/pub/pdb/validation_reports/t5/1t5m | 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 | Type: Cyclic lipopeptide / Class: Antibiotic / Mass: 1484.440 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: DAPTOMYCIN IS AN ACIDIC CYCLIC LIPOPEPTIDE. THE SCAFFOLD IS MADE OF TWO PARTS: (1) THREE RESIDUES N-TERM EXOCYCLIC PART (2) A DECAPEPTIDE LACTONE RING DERIVED FROM CYCLISATION OF THR3 SIDE ...Details: DAPTOMYCIN IS AN ACIDIC CYCLIC LIPOPEPTIDE. THE SCAFFOLD IS MADE OF TWO PARTS: (1) THREE RESIDUES N-TERM EXOCYCLIC PART (2) A DECAPEPTIDE LACTONE RING DERIVED FROM CYCLISATION OF THR3 SIDE CHAIN ONTO THE C-TER CARBOXYL GROUP THE N-DECANOYL FATTY ACID IS LINKED TO THE MAIN BODY OF THE MOLECULE VIA N-TERM ACYLATION. Source: (synth.) STREPTOMYCES ROSEOSPORUS (bacteria) / References: NOR: NOR00001, Daptomycin |
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#2: Chemical | ChemComp-DKA / Type: Cyclic lipopeptide / Class: Antibiotic / Mass: 172.265 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H20O2 Details: DAPTOMYCIN IS AN ACIDIC CYCLIC LIPOPEPTIDE. THE SCAFFOLD IS MADE OF TWO PARTS: (1) THREE RESIDUES N-TERM EXOCYCLIC PART (2) A DECAPEPTIDE LACTONE RING DERIVED FROM CYCLISATION OF THR3 SIDE ...Details: DAPTOMYCIN IS AN ACIDIC CYCLIC LIPOPEPTIDE. THE SCAFFOLD IS MADE OF TWO PARTS: (1) THREE RESIDUES N-TERM EXOCYCLIC PART (2) A DECAPEPTIDE LACTONE RING DERIVED FROM CYCLISATION OF THR3 SIDE CHAIN ONTO THE C-TER CARBOXYL GROUP THE N-DECANOYL FATTY ACID IS LINKED TO THE MAIN BODY OF THE MOLECULE VIA N-TERM ACYLATION. References: Daptomycin |
Compound details | DAPTOMYCIN IS A CYCLIC TRIDECAMER LIPOPETIDE. HERE, DAPTOMYCIN IS REPRESENTED BY GROUPING TOGETHER ...DAPTOMYCIN |
-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: 2MM DAPTOMYCIN, 100MM KCL, 2MM EGTA, 0.2MM EDTA, 93% H2O, 7% D2O |
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Sample conditions | Ionic strength: 100mM KCL / pH: 6.6 / Pressure: AMBIENT / Temperature: 290.15 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 500 MHz |
-Processing
NMR software |
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NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 50 / Conformers submitted total number: 15 |