+Open data
-Basic information
Entry | Database: PDB / ID: 4d6u | |||||||||
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Title | Cytochrome bc1 bound to the 4(1H)-pyridone GSK932121 | |||||||||
Components |
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Keywords | OXIDOREDUCTASE / MEMBRANE PROTEIN / COMPLEX | |||||||||
Function / homology | Function and homology information mitochondrial respiratory chain complex III assembly / Respiratory electron transport / mitochondrial respiratory chain complex III / mitochondrial respiratory chain complex IV / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / ubiquinone binding / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / respiratory electron transport chain ...mitochondrial respiratory chain complex III assembly / Respiratory electron transport / mitochondrial respiratory chain complex III / mitochondrial respiratory chain complex IV / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / ubiquinone binding / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / respiratory electron transport chain / mitochondrial membrane / 2 iron, 2 sulfur cluster binding / metalloendopeptidase activity / mitochondrial inner membrane / oxidoreductase activity / heme binding / mitochondrion / proteolysis / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | BOS TAURUS (cattle) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.09 Å | |||||||||
Authors | 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. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4d6u.cif.gz | 815.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4d6u.ent.gz | 642.6 KB | Display | PDB format |
PDBx/mmJSON format | 4d6u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d6/4d6u ftp://data.pdbj.org/pub/pdb/validation_reports/d6/4d6u | HTTPS FTP |
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-Related structure data
Related structure data | 4d6tC 1ppjS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-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) BOS TAURUS (cattle) / Organ: HEART / Tissue: MUSCLESkeletal muscle / References: UniProt: P31800 | ||||||||||||||
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#2: Protein | Mass: 48203.434 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Tissue: MUSCLESkeletal muscle / References: UniProt: P23004 | ||||||||||||||
#5: Protein | Mass: 29586.842 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Tissue: MUSCLESkeletal muscle / References: UniProt: P13272, quinol-cytochrome-c reductase #6: Protein | Mass: 13502.387 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Tissue: MUSCLESkeletal muscle / References: UniProt: P00129 #7: Protein | Mass: 9737.223 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Tissue: MUSCLESkeletal muscle / References: UniProt: P13271 #8: Protein | Mass: 10638.744 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Tissue: MUSCLESkeletal muscle / References: UniProt: P00126 #9: Protein | Mass: 7469.621 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Tissue: MUSCLESkeletal muscle / References: UniProt: P00130 #10: Protein | | Mass: 52768.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Tissue: MUSCLESkeletal muscle / References: UniProt: P31800 #11: Protein | | Mass: 48204.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Tissue: MUSCLESkeletal muscle / References: UniProt: P23004 #12: Protein | | Mass: 29572.814 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Tissue: MUSCLESkeletal muscle / References: UniProt: P13272, quinol-cytochrome-c reductase |
-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) BOS TAURUS (cattle) / Organ: HEART / Tissue: MUSCLESkeletal muscle / References: UniProt: P00157 #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) BOS TAURUS (cattle) / Organ: HEART / Tissue: MUSCLESkeletal muscle / References: UniProt: P00125 |
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-Non-polymers , 8 types, 27 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.979 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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