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- PDB-7zed: Solution structure of thanatin-like derivative 7 in complex with ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7zed | ||||||||||||
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Title | Solution structure of thanatin-like derivative 7 in complex with E.coli LptA mutant Q62L | ||||||||||||
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![]() | ANTIBIOTIC / STRUCTURE FROM CYANA 3.98.11 | ||||||||||||
Function / homology | ![]() transporter complex / glycolipid transfer activity / lipopolysaccharide transport / Gram-negative-bacterium-type cell outer membrane assembly / defense response to fungus / lipopolysaccharide binding / cell outer membrane / outer membrane-bounded periplasmic space / killing of cells of another organism / periplasmic space ...transporter complex / glycolipid transfer activity / lipopolysaccharide transport / Gram-negative-bacterium-type cell outer membrane assembly / defense response to fungus / lipopolysaccharide binding / cell outer membrane / outer membrane-bounded periplasmic space / killing of cells of another organism / periplasmic space / defense response to bacterium / innate immune response / extracellular region / identical protein binding Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||
Method | SOLUTION NMR / na | ||||||||||||
![]() | Moehle, K. / Zerbe, O. | ||||||||||||
Funding support | European Union, 1items
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![]() | ![]() Title: Peptidomimetic antibiotics disrupt the lipopolysaccharide transport bridge of drug-resistant Enterobacteriaceae. Authors: Schuster, M. / Brabet, E. / Oi, K.K. / Desjonqueres, N. / Moehle, K. / Le Poupon, K. / Hell, S. / Gable, S. / Rithie, V. / Dillinger, S. / Zbinden, P. / Luther, A. / Li, C. / Stiegeler, S. / ...Authors: Schuster, M. / Brabet, E. / Oi, K.K. / Desjonqueres, N. / Moehle, K. / Le Poupon, K. / Hell, S. / Gable, S. / Rithie, V. / Dillinger, S. / Zbinden, P. / Luther, A. / Li, C. / Stiegeler, S. / D'Arco, C. / Locher, H. / Remus, T. / DiMaio, S. / Motta, P. / Wach, A. / Jung, F. / Upert, G. / Obrecht, D. / Benghezal, M. / Zerbe, O. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 808.3 KB | Display | ![]() |
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PDB format | ![]() | 679.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 429.9 KB | Display | ![]() |
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Full document | ![]() | 676.2 KB | Display | |
Data in XML | ![]() | 42.9 KB | Display | |
Data in CIF | ![]() | 72.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7qs6C ![]() 7zaxC ![]() 8bssC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: Protein | Mass: 12853.328 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The sequence doesnt contain the signaling sequence (Residues 1-27 from UNIPROT entry P0ADV1). The first residue is numbered 28. The expressed construct is 28-159. Deposited are coordinates ...Details: The sequence doesnt contain the signaling sequence (Residues 1-27 from UNIPROT entry P0ADV1). The first residue is numbered 28. The expressed construct is 28-159. Deposited are coordinates for the structured part containing residues 28-145. Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 2007.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
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: 300 uM [U-13C; U-15N] Lipopolysaccharide export system protein LptA, 20 mM sodium phosphate, 150 mM sodium chloride, 90% H2O/10% D2O Details: 13C,15N-labelled LptA-Q62L (28-145) / Label: LptAm_15N13C / Solvent system: 90% H2O/10% D2O | ||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 150 mM / Ionic strength err: 10 / Label: conditions_1 / pH: 7.0 / PH err: 0.1 / Pressure: 1 atm / Pressure err: 0.01 / Temperature: 298 K / Temperature err: 0.2 |
-NMR measurement
NMR spectrometer |
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Processing
NMR software |
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Refinement | Method: na / Software ordinal: 1 | ||||||||||||||||||||||||
NMR representative | Selection criteria: target function | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |