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Open data
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Basic information
Entry | Database: PDB / ID: 4d6u | |||||||||
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Title | Cytochrome bc1 bound to the 4(1H)-pyridone GSK932121 | |||||||||
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![]() | OXIDOREDUCTASE / MEMBRANE PROTEIN / COMPLEX | |||||||||
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 | ![]() ![]() ![]() | |||||||||
![]() | Capper, M.J. / ONeill, P.M. / Fisher, N. / Strange, R.W. / Moss, D. / Ward, S.A. / Berry, N.G. / Lawrenson, A.S. / Hasnain, S.S. / Biagini, G.A. / Antonyuk, S.V. | |||||||||
![]() | ![]() Title: Antimalarial 4(1H)-Pyridones Bind to the Qi Site of Cytochrome Bc1. Authors: Capper, M.J. / O'Neill, P.M. / Fisher, N. / Strange, R.W. / Moss, D. / Ward, S.A. / Berry, N.G. / Lawrenson, A.S. / Hasnain, S.S. / Biagini, G.A. / Antonyuk, S.V. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 815.8 KB | Display | ![]() |
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PDB format | ![]() | 642.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4d6tC ![]() 1ppjS C: citing same article ( S: Starting model for refinement |
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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
-CYTOCHROME B-C1 COMPLEX SUBUNIT ... , 10 types, 16 molecules ABEIRFSGTHUJWNOV
#1: Protein | Mass: 52796.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||||||||||||
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#2: Protein | Mass: 48203.434 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||||||||||||
#5: Protein | Mass: 29586.842 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #6: Protein | Mass: 13502.387 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #7: Protein | Mass: 9737.223 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #8: Protein | Mass: 10638.744 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #9: Protein | Mass: 7469.621 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #10: Protein | | Mass: 52768.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #11: Protein | | Mass: 48204.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #12: Protein | | Mass: 29572.814 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Protein , 2 types, 4 molecules CPDQ
#3: Protein | Mass: 42620.340 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #4: Protein | Mass: 35343.770 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: THE 4(1H)-PYRIDONE, GSK932121, BOUND IN THE QI SITE OF CYTOCHROME B Source: (natural) ![]() ![]() |
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-Non-polymers , 8 types, 27 molecules ![](data/chem/img/HEM.gif)
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![](data/chem/img/PO4.gif)
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![](data/chem/img/FES.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/G8U.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/PEE.gif)
![](data/chem/img/HEC.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/GOL.gif)
#13: Chemical | ChemComp-HEM / #14: Chemical | #15: Chemical | ChemComp-PO4 / #16: Chemical | ChemComp-PEE / #17: Chemical | #18: Chemical | ChemComp-CDL / #19: Chemical | ChemComp-FES / | #20: Chemical | ChemComp-GOL / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 34.7 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 6.8 Details: SITTING DROP VAPOUR DIFFUSION 50 MM KPI, PH 6.8, 100 MM NACL, 3 MM NAN3, 10 - 13 % PEG4000,1.4% HECAMEG |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 21, 2013 / Details: MIRRORS |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 4.09→42.1 Å / Num. obs: 42955 / % possible obs: 80.7 % / Redundancy: 3.2 % / Biso Wilson estimate: 123.66 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 6 |
Reflection shell | Resolution: 4.09→4.25 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.55 / % possible all: 51.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1PPJ Resolution: 4.09→50 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.852 / Cross valid method: THROUGHOUT / ESU R Free: 1.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: 162.551 Å2
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Refinement step | Cycle: LAST / Resolution: 4.09→50 Å
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