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Yorodumi- PDB-8onu: Solution structure of thanatin analogue 7 in complex with LptAm(Ab)1.0 -
+Open data
-Basic information
Entry | Database: PDB / ID: 8onu | |||||||||
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Title | Solution structure of thanatin analogue 7 in complex with LptAm(Ab)1.0 | |||||||||
Components |
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Keywords | ANTIBIOTIC / STRUCTURE FROM CYANA 3.98.13 | |||||||||
Function / homology | Function and homology information lipopolysaccharide transport / Gram-negative-bacterium-type cell outer membrane assembly / defense response to fungus / lipopolysaccharide binding / killing of cells of another organism / periplasmic space / defense response to bacterium / innate immune response / extracellular region Similarity search - Function | |||||||||
Biological species | Acinetobacter baumannii (bacteria) Podisus maculiventris (spined soldier bug) | |||||||||
Method | SOLUTION NMR / molecular dynamics | |||||||||
Authors | Oi, K.K. / Moehle, K. / Zerbe, O. | |||||||||
Funding support | European Union, 1items
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Citation | Journal: Molecules / Year: 2023 Title: Early Molecular Insights into Thanatin Analogues Binding to A. baumannii LptA. Authors: Oi, K.K. / Moehle, K. / Schuster, M. / Zerbe, O. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8onu.cif.gz | 904.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8onu.ent.gz | 753.5 KB | Display | PDB format |
PDBx/mmJSON format | 8onu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8onu_validation.pdf.gz | 430.5 KB | Display | wwPDB validaton report |
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Full document | 8onu_full_validation.pdf.gz | 671.7 KB | Display | |
Data in XML | 8onu_validation.xml.gz | 63.1 KB | Display | |
Data in CIF | 8onu_validation.cif.gz | 80.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/on/8onu ftp://data.pdbj.org/pub/pdb/validation_reports/on/8onu | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | Similarity search - Function & homologyF&H Search |
Other databases |
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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 | Mass: 14265.767 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Strain: DH5a Gene: lptA, A7M90_06575, AB945B12_03460, ABCAM1_1308, ABKPCSM17A_03058, ABR2091_1232, ABUW_2646, ACX61_12145, APD31_17240, AUO97_13655, AYR68_06125, B7L45_12725, B9X95_15845, BAA1790NC_1298, C6N18_ ...Gene: lptA, A7M90_06575, AB945B12_03460, ABCAM1_1308, ABKPCSM17A_03058, ABR2091_1232, ABUW_2646, ACX61_12145, APD31_17240, AUO97_13655, AYR68_06125, B7L45_12725, B9X95_15845, BAA1790NC_1298, C6N18_07050, CBE85_10985, CBL15_11855, CSB70_1068, CTZ19_12250, D8O08_008535, DLI71_18810, DOL94_11450, DVA69_07650, E1A86_07710, E1A87_18595, EA686_18135, EA706_10880, EA720_004080, EA722_14830, EGM95_13940, EKS29_04650, EWO96_18090, F2P40_12435, F4T85_13200, FDN00_13585, FE003_12605, FJU36_12005, FJU42_14040, FR761_07300, G3N53_13510, GNY86_07325, GSE42_07235, H0529_08305, HB367_02715, HBK86_04580, HIN86_12575, IAG11_06185, IMO23_06220, ITE13_09135, NCTC13305_01082, NCTC13421_02501, SAMEA104305318_02787, SAMEA104305340_03609, SAMEA104305385_03383 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: V5VEZ9 |
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#2: Protein/peptide | Mass: 2007.387 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: VAN = valine capped with guanidine group, HYP = hydroxyproline, LE1 = penicillamine, DAB = diaminobutyric acid, 4FO = D-DAB Source: (synth.) Podisus maculiventris (spined soldier bug) / References: UniProt: P55788 |
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] A. baumannii lipopolysaccharide transport protein A (LptA) (33-164), 500 uM Thanatin analogue 7, 50 mM sodium phosphate, 150 mM sodium chloride, 90% H2O/10% D2O Details: 13C, 15N-labelled LptAm(33-150) / 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 / 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: molecular dynamics / Software ordinal: 2 | ||||||||||||||||||||
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 |