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- PDB-5tlq: Model structure of the oxidized PaDsbA1 and 3-[(2-methylbenzyl)su... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5tlq | |||||||||
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Title | Model structure of the oxidized PaDsbA1 and 3-[(2-methylbenzyl)sulfanyl]-4H-1,2,4-triazol-4-amine complex | |||||||||
![]() | Thiol:disulfide interchange protein DsbA | |||||||||
![]() | OXIDOREDUCTASE / oxidised PaDsbA1 / 3-((2-methylbenzyl)thio)-4H-1 / 2 / 4-triazol-4-amine / HADDOCK docking | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | SOLUTION NMR / simulated annealing | |||||||||
![]() | Mohanty, B. / Rimmer, K.A. / McMahon, R.M. / Headey, S.J. / Vazirani, M. / Shouldice, S.R. / Coincon, M. / Tay, S. / Morton, C.J. / Simpson, J.S. ...Mohanty, B. / Rimmer, K.A. / McMahon, R.M. / Headey, S.J. / Vazirani, M. / Shouldice, S.R. / Coincon, M. / Tay, S. / Morton, C.J. / Simpson, J.S. / Martin, J.L. / Scanlon, M.S. | |||||||||
![]() | ![]() Title: Fragment library screening identifies hits that bind to the non-catalytic surface of Pseudomonas aeruginosa DsbA1. Authors: Mohanty, B. / Rimmer, K. / McMahon, R.M. / Headey, S.J. / Vazirani, M. / Shouldice, S.R. / Coincon, M. / Tay, S. / Morton, C.J. / Simpson, J.S. / Martin, J.L. / Scanlon, M.J. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 644.1 KB | Display | ![]() |
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PDB format | ![]() | 547.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 452.9 KB | Display | ![]() |
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Full document | ![]() | 513.7 KB | Display | |
Data in XML | ![]() | 39.6 KB | Display | |
Data in CIF | ![]() | 51.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2mbtC ![]() 5dchC C: citing same article ( |
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Similar structure data | |
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: 21152.260 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: dsbA, PA5489 / Plasmid: pET28a / Cell line (production host): BL21(DE3)-Gold / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-1YO / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||
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NMR experiment |
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Sample preparation
Details | Type: solution Contents: 0.3 mM [U-98% 13C; U-98% 15N] PaDsbA1, 3.3 mM 3-((2-methylbenzyl)thio)-4H-1,2,4-triazol-4-amine, 97.3%D2O+1.7%D6-DMSO Details: 300 uM PaDsbA1; 3.3 mM 3-((2-methylbenzyl)thio)-4H-1,2,4-triazol-4-amine; 1.7% D6-DMSO; 50 mM sodium Phosphate; 50 mM sodium Chloride; 0.02% sodium azide Label: [U-13C,15N] PaDsbA1 and unlabelled 3-((2-methylbenzyl)thio)-4H-1,2,4-triazol-4-amine Solvent system: 97.3%D2O+1.7%D6-DMSO | ||||||||||||
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Sample |
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Sample conditions | Details: 300 uM PaDsbA1; 3.3 mM 3-((2-methylbenzyl)thio)-4H-1,2,4-triazol-4-amine; 1.7% D6-DMSO; 50 mM sodium phosphate; 50 mM sodium Chloride; 0.02% sodium azide Ionic strength: 50 mM NaCl and 50 mM sodium phosphate Not defined Label: condition_1 / pH: 7.4 / Pressure: 1 bar / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 800 MHz |
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Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 3 Details: 2MBT from the same group was used for HADDOCK model building | ||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 10 |