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- PDB-4p8m: Crystal structure of M. tuberculosis DprE1 in complex with the no... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4p8m | ||||||
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Title | Crystal structure of M. tuberculosis DprE1 in complex with the non-covalent inhibitor QN114 | ||||||
![]() | Probable decaprenylphosphoryl-beta-D-ribose oxidase | ||||||
![]() | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / DprE1 / inhibitor / complex / non-covalent / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex | ||||||
Function / homology | ![]() arabinan biosynthetic process / cell wall polysaccharide biosynthetic process / decaprenylphospho-beta-D-ribofuranose 2-dehydrogenase / D-arabinono-1,4-lactone oxidase activity / capsule polysaccharide biosynthetic process / FAD binding / cell wall organization / periplasmic space / oxidoreductase activity / response to antibiotic ...arabinan biosynthetic process / cell wall polysaccharide biosynthetic process / decaprenylphospho-beta-D-ribofuranose 2-dehydrogenase / D-arabinono-1,4-lactone oxidase activity / capsule polysaccharide biosynthetic process / FAD binding / cell wall organization / periplasmic space / oxidoreductase activity / response to antibiotic / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Neres, J. / Pojer, F. / Cole, S.T. | ||||||
Funding support | ![]()
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![]() | ![]() Title: 2-Carboxyquinoxalines Kill Mycobacterium tuberculosis through Noncovalent Inhibition of DprE1. Authors: Neres, J. / Hartkoorn, R.C. / Chiarelli, L.R. / Gadupudi, R. / Pasca, M.R. / Mori, G. / Venturelli, A. / Savina, S. / Makarov, V. / Kolly, G.S. / Molteni, E. / Binda, C. / Dhar, N. / ...Authors: Neres, J. / Hartkoorn, R.C. / Chiarelli, L.R. / Gadupudi, R. / Pasca, M.R. / Mori, G. / Venturelli, A. / Savina, S. / Makarov, V. / Kolly, G.S. / Molteni, E. / Binda, C. / Dhar, N. / Ferrari, S. / Brodin, P. / Delorme, V. / Landry, V. / de Jesus Lopes Ribeiro, A.L. / Farina, D. / Saxena, P. / Pojer, F. / Carta, A. / Luciani, R. / Porta, A. / Zanoni, G. / De Rossi, E. / Costi, M.P. / Riccardi, G. / Cole, S.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 183.1 KB | Display | ![]() |
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PDB format | ![]() | 141.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 33.7 KB | Display | |
Data in CIF | ![]() | 46.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4cvyC ![]() 4p8cC ![]() 4p8kC ![]() 4p8lC ![]() 4p8nC ![]() 4p8pC ![]() 4p8tC ![]() 4p8yC 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 52260.133 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P72056, UniProt: P9WJF0*PLUS, Oxidoreductases |
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-Non-polymers , 5 types, 205 molecules ![](data/chem/img/FAD.gif)
![](data/chem/img/R58.gif)
![](data/chem/img/2J3.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/R58.gif)
![](data/chem/img/2J3.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-2J3 / ( | #5: Chemical | ChemComp-IMD / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.63 % / Description: Rmeas 0.078 (overall), 0.465 (outer shell) |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.9 / Details: 39% polypropyleneglycol, 100 mM imidazole |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 13, 2014 |
Radiation | Monochromator: Bartels monochromator with dual channel cut crystals Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→47.9 Å / Num. obs: 97109 / % possible obs: 96.3 % / Redundancy: 2.7 % / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.09→2.22 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2.79 / % possible all: 90.4 |
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Processing
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Refinement | Resolution: 2.09→47.9 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.046 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.235 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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 mean: 33.236 Å2
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Refinement step | Cycle: 1 / Resolution: 2.09→47.9 Å
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Refine LS restraints |
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