[English] 日本語
![](img/lk-miru.gif)
- PDB-7r3v: Crystal structure of bovine Cytochrome bc1 in complex with inhibi... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7r3v | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of bovine Cytochrome bc1 in complex with inhibitor CK-2-67. | |||||||||
![]() |
| |||||||||
![]() | ELECTRON TRANSPORT | |||||||||
Function / homology | ![]() Respiratory electron transport / : / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / Mitochondrial protein degradation / ubiquinone binding / : / respiratory electron transport chain / mitochondrial membrane ...Respiratory electron transport / : / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / Mitochondrial protein degradation / ubiquinone binding / : / respiratory electron transport chain / mitochondrial membrane / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / mitochondrial inner membrane / oxidoreductase activity / heme binding / mitochondrion / proteolysis / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Pinthong, N. / Amporndanai, K. / O'Neill, P.M. / Hasnain, S.S. / Antonyuk, S. | |||||||||
Funding support | 1items
| |||||||||
![]() | ![]() Title: Targeting the Ubiquinol-Reduction (Q i ) Site of the Mitochondrial Cytochrome bc 1 Complex for the Development of Next Generation Quinolone Antimalarials. Authors: Amporndanai, K. / Pinthong, N. / O'Neill, P.M. / Hong, W.D. / Amewu, R.K. / Pidathala, C. / Berry, N.G. / Leung, S.C. / Ward, S.A. / Biagini, G.A. / Hasnain, S.S. / Antonyuk, S.V. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 441.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 342 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 5okdS S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Cytochrome b-c1 complex subunit ... , 8 types, 8 molecules ABEFGHIJ
#1: Protein | Mass: 49209.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
---|---|
#2: Protein | Mass: 44495.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#5: Protein | Mass: 21640.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#6: Protein | Mass: 12357.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#7: Protein | Mass: 8799.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#8: Protein | Mass: 7628.592 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#9: Protein/peptide | Mass: 4827.567 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#10: Protein | Mass: 6866.897 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Protein , 2 types, 2 molecules CD
#3: Protein | Mass: 42620.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
---|---|
#4: Protein | Mass: 27107.021 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Sugars , 1 types, 1 molecules ![](data/chem/img/LMT.gif)
#15: Sugar | ChemComp-LMT / |
---|
-Non-polymers , 12 types, 70 molecules ![](data/chem/img/PG4.gif)
![](data/chem/img/6PE.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/PEE.gif)
![](data/chem/img/I2Q.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HEC.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/PX4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/6PE.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/PEE.gif)
![](data/chem/img/I2Q.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HEC.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/PX4.gif)
![](data/chem/img/HOH.gif)
#11: Chemical | #12: Chemical | ChemComp-6PE / | #13: Chemical | #14: Chemical | #16: Chemical | #17: Chemical | ChemComp-I2Q / | #18: Chemical | ChemComp-DMS / | #19: Chemical | ChemComp-PO4 / #20: Chemical | ChemComp-HEC / | #21: Chemical | ChemComp-FES / | #22: Chemical | ChemComp-PX4 / | #23: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 4.72 Å3/Da / Density % sol: 73.93 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: Protein 40mg/mL with 1.6% HECAMEG; reservoir solution 50mM KPi pH 6.8, 100mM NaCl, 3mM NaN3, 9-12% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 21, 2020 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→49.86 Å / Num. obs: 70108 / % possible obs: 97.2 % / Redundancy: 9.4 % / CC1/2: 0.993 / Rpim(I) all: 0.064 / Rrim(I) all: 0.225 / Χ2: 0.98 / Net I/av σ(I): 8.5 / Net I/σ(I): 1.7 |
Reflection shell | Resolution: 3.2→3.27 Å / Redundancy: 4.9 % / Rmerge(I) obs: 1.597 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4544 / CC1/2: 0.415 / Rpim(I) all: 0.498 / Rrim(I) all: 1.718 / Χ2: 1.06 / % possible all: 97.2 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5OKD Resolution: 3.2→49.86 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.89 / SU B: 21.345 / SU ML: 0.336 / Cross valid method: THROUGHOUT / ESU R: 2.704 / ESU R Free: 0.42 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 86.4 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 3.2→49.86 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|