+Open data
-Basic information
Entry | Database: PDB / ID: 1xt7 | ||||||
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Title | Daptomycin NMR Structure | ||||||
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 / CONSTRAINED MOLECULAR DYNAMICS | ||||||
Authors | Ball, L.-J. / Goult, C.M. / Donarski, J.A. / Micklefield, J. / Ramesh, V. | ||||||
Citation | Journal: Org.Biomol.Chem. / Year: 2004 Title: NMR Structure Determination and Calcium Binding Effects of Lipopeptide Antibiotic Daptomycin Authors: Ball, L.-J. / Goult, C.M. / Donarski, J.A. / Micklefield, J. / Ramesh, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xt7.cif.gz | 10.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xt7.ent.gz | 8.3 KB | Display | PDB format |
PDBx/mmJSON format | 1xt7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1xt7_validation.pdf.gz | 359.3 KB | Display | wwPDB validaton report |
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Full document | 1xt7_full_validation.pdf.gz | 359.2 KB | Display | |
Data in XML | 1xt7_validation.xml.gz | 2.2 KB | Display | |
Data in CIF | 1xt7_validation.cif.gz | 2.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xt/1xt7 ftp://data.pdbj.org/pub/pdb/validation_reports/xt/1xt7 | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar 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 | Type: 2D NOESY |
NMR details | Text: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR TECHNIQUES. |
-Sample preparation
Details |
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Sample conditions | pH: 5.05 / Pressure: AMBIENT / Temperature: 298 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: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz |
-Processing
NMR software |
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Refinement | Method: CONSTRAINED MOLECULAR DYNAMICS / Software ordinal: 1 Details: A TOTAL OF 52 DISTANCE RESTRAINTS WERE USED FOR NMR STRUCTURE CALCULATION. | ||||||||||||||||||
NMR ensemble | Conformers submitted total number: 1 |