[English] 日本語
![](img/lk-miru.gif)
- PDB-5oip: InhA (T2A mutant) complexed with 1-(Pyridin-3-ylmethyl)-3-(1-(pyr... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5oip | ||||||
---|---|---|---|---|---|---|---|
Title | InhA (T2A mutant) complexed with 1-(Pyridin-3-ylmethyl)-3-(1-(pyrimidin-2-yl)piperidin-4-yl)urea | ||||||
![]() | Enoyl-[acyl-carrier-protein] reductase [NADH] | ||||||
![]() | OXIDOREDUCTASE / Inhibitor / complex / fragment based drug discovery / tuberculosis | ||||||
Function / homology | ![]() trans-2-enoyl-CoA reductase (NADH) activity / mycolic acid biosynthetic process / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / NAD+ binding / peptidoglycan-based cell wall / fatty acid binding / response to antibiotic / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Convery, M.A. | ||||||
![]() | ![]() Title: Screening of a Novel Fragment Library with Functional Complexity against Mycobacterium tuberculosis InhA. Authors: Prati, F. / Zuccotto, F. / Fletcher, D. / Convery, M.A. / Fernandez-Menendez, R. / Bates, R. / Encinas, L. / Zeng, J. / Chung, C.W. / De Dios Anton, P. / Mendoza-Losana, A. / Mackenzie, C. / ...Authors: Prati, F. / Zuccotto, F. / Fletcher, D. / Convery, M.A. / Fernandez-Menendez, R. / Bates, R. / Encinas, L. / Zeng, J. / Chung, C.W. / De Dios Anton, P. / Mendoza-Losana, A. / Mackenzie, C. / Green, S.R. / Huggett, M. / Barros, D. / Wyatt, P.G. / Ray, P.C. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 127.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 98.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 5oicC ![]() 5oifC ![]() 5oilC ![]() 5oimC ![]() 5oinC ![]() 5oioC ![]() 5oiqC ![]() 5oirC ![]() 5oisC ![]() 5oitC C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 28524.754 Da / Num. of mol.: 1 / Mutation: T2A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P9WGR1, enoyl-[acyl-carrier-protein] reductase (NADH) |
---|---|
#2: Chemical | ChemComp-NAD / |
#3: Chemical | ChemComp-9WE / |
#4: Chemical | ChemComp-PO4 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.52 Å3/Da / Density % sol: 65.05 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 10% glycerol, 25% 1,2propanediol, 0.1M PO4. Cryo is well solution |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 22, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9282 Å / Relative weight: 1 |
Reflection | Resolution: 1.71→41.34 Å / Num. obs: 45004 / % possible obs: 99.9 % / Redundancy: 19.2 % / Biso Wilson estimate: 31.31 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.101 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 1.71→1.75 Å / Redundancy: 17.1 % / Rmerge(I) obs: 2.876 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3248 / CC1/2: 0.514 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.71→25.04 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.966 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.078 / SU Rfree Blow DPI: 0.073 / SU Rfree Cruickshank DPI: 0.069
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.29 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.71→25.04 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.71→1.75 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 45.8577 Å / Origin y: 48.705 Å / Origin z: -88.9066 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: { A|* } |