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- PDB-9rf5: M. tuberculosis meets European Lead Factory: identification and s... -
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Open data
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Basic information
Entry | Database: PDB / ID: 9rf5 | ||||||||||||
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Title | M. tuberculosis meets European Lead Factory: identification and structural characterization of novel Rv0183 inhibitors using X-ray crystallography: ELF8 | ||||||||||||
![]() | Monoacylglycerol lipase | ||||||||||||
![]() | HYDROLASE / Rv0183 / Inhibitor / Monoacylglycerol lipase | ||||||||||||
Function / homology | ![]() glycerolipid catabolic process / acylglycerol lipase / lipase activity / monoacylglycerol lipase activity / peptidoglycan-based cell wall / symbiont-mediated activation of host apoptosis / extracellular region / membrane / plasma membrane Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Riegler-Berket, L. / Goedl, L. / Oberer, M. / Polidori, N. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: M. tuberculosis meets European Lead Factory: identification and structural characterization of novel Rv0183 inhibitors using X-ray crystallography Authors: Riegler-Berket, L. / Goedl, L. / Oberer, M. / Polidori, N. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 74 KB | Display | ![]() |
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PDB format | ![]() | 52.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 751.3 KB | Display | ![]() |
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Full document | ![]() | 753.1 KB | Display | |
Data in XML | ![]() | 14.8 KB | Display | |
Data in CIF | ![]() | 19.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9rf2C C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 33618.047 Da / Num. of mol.: 1 / Mutation: K74A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: Rv0183 / Production host: ![]() ![]() |
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-Non-polymers , 6 types, 86 molecules 








#2: Chemical | ChemComp-8D5 / [( Mass: 418.366 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H17F3N2O4 / Feature type: SUBJECT OF INVESTIGATION |
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#3: Chemical | ChemComp-MPD / ( |
#4: Chemical | ChemComp-EDO / |
#5: Chemical | ChemComp-PGE / |
#6: Chemical | ChemComp-PEG / |
#7: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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Has protein modification | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 30.09 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PEG 1000, PEG 3350, MPD, HEPES, MOPS, CHAPS, CHAPSO, Sodium glycocholate hydrate, Taurocholic acid sodium salt hydrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 22, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03323 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→37.65 Å / Num. obs: 29055 / % possible obs: 99.85 % / Redundancy: 2 % / Biso Wilson estimate: 19.49 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.01921 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 1.8→1.864 Å / Num. unique obs: 2845 / CC1/2: 0.959 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.61 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→37.65 Å
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Refine LS restraints |
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LS refinement shell |
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