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- PDB-7oum: BDM88855 inhibitor bound to the transmembrane domain of AcrB-R971A -
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Open data
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Basic information
Entry | Database: PDB / ID: 7oum | ||||||
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Title | BDM88855 inhibitor bound to the transmembrane domain of AcrB-R971A | ||||||
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![]() | TRANSPORT PROTEIN / Multidrug efflux pump / Membrane protein | ||||||
Function / homology | ![]() xenobiotic detoxification by transmembrane export across the cell outer membrane / efflux pump complex / periplasmic side of plasma membrane / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / outer membrane-bounded periplasmic space / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tam, H.K. / Foong, W.E. / Pos, K.M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Pyridylpiperazine-based allosteric inhibitors of RND-type multidrug efflux pumps. Authors: Ple, C. / Tam, H.K. / Vieira Da Cruz, A. / Compagne, N. / Jimenez-Castellanos, J.C. / Muller, R.T. / Pradel, E. / Foong, W.E. / Malloci, G. / Ballee, A. / Kirchner, M.A. / Moshfegh, P. / ...Authors: Ple, C. / Tam, H.K. / Vieira Da Cruz, A. / Compagne, N. / Jimenez-Castellanos, J.C. / Muller, R.T. / Pradel, E. / Foong, W.E. / Malloci, G. / Ballee, A. / Kirchner, M.A. / Moshfegh, P. / Herledan, A. / Herrmann, A. / Deprez, B. / Willand, N. / Vargiu, A.V. / Pos, K.M. / Flipo, M. / Hartkoorn, R.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.3 MB | Display | ![]() |
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PDB format | ![]() | 1.1 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.6 MB | Display | ![]() |
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Full document | ![]() | 2.6 MB | Display | |
Data in XML | ![]() | 116.4 KB | Display | |
Data in CIF | ![]() | 161.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7oukC ![]() 7oulC ![]() 5jmnS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 2 types, 5 molecules ABCDE
#1: Protein | Mass: 114650.180 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 18317.566 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Gene: ARTIFICIAL GENE / Plasmid: PQE30 / Production host: ![]() ![]() |
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-Sugars , 1 types, 7 molecules ![](data/chem/img/LMT.gif)
#3: Sugar | ChemComp-LMT / |
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-Non-polymers , 10 types, 707 molecules ![](data/chem/img/C14.gif)
![](data/chem/img/DDQ.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/1K8.gif)
![](data/chem/img/D10.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/OCT.gif)
![](data/chem/img/LPX.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DDQ.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/1K8.gif)
![](data/chem/img/D10.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/OCT.gif)
![](data/chem/img/LPX.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-C14 / | ||||||||||||||||
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#5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-D10 / #9: Chemical | ChemComp-EDO / #10: Chemical | #11: Chemical | ChemComp-OCT / #12: Chemical | ChemComp-LPX / ( | #13: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.9 Å3/Da / Density % sol: 68.51 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: 0.05M ADA, PH 6.6, 0.13-0.2M AMMONIUM SULFATE, 5% GLYCEROL, 8-9% PEG4000, 0.006M BDM88855 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 14, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.45→49.51 Å / Num. obs: 212143 / % possible obs: 100 % / Redundancy: 13.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.281 / Rpim(I) all: 0.078 / Rrim(I) all: 0.292 / Net I/σ(I): 6.5 / Num. measured all: 2939346 / Scaling rejects: 1264 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5JMN Resolution: 2.45→49.51 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.892 / WRfactor Rfree: 0.2547 / WRfactor Rwork: 0.2268 / FOM work R set: 0.7838 / SU B: 19.349 / SU ML: 0.212 / SU R Cruickshank DPI: 0.3068 / SU Rfree: 0.2336 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.307 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 116.83 Å2 / Biso mean: 49.147 Å2 / Biso min: 20.62 Å2
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Refinement step | Cycle: final / Resolution: 2.45→49.51 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.45→2.513 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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