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- PDB-3ag1: Bovine Heart Cytochrome c Oxidase in the Carbon Monoxide-bound Fu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ag1 | ||||||
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Title | Bovine Heart Cytochrome c Oxidase in the Carbon Monoxide-bound Fully Reduced State at 280 K | ||||||
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![]() | OXIDOREDUCTASE / Copper / Electron transport / Formylation / Heme / Iron / Membrane / Mitochondrion / Mitochondrion inner membrane / Respiratory chain / Transmembrane / Transport / Acetylation / Transit peptide / Zinc / Isopeptide bond / Ubl conjugation | ||||||
Function / homology | ![]() TP53 Regulates Metabolic Genes / Cytoprotection by HMOX1 / respiratory chain complex IV assembly / mitochondrial respirasome assembly / respiratory chain complex IV / mitochondrial respiratory chain complex IV / regulation of oxidative phosphorylation / Respiratory electron transport / cytochrome-c oxidase / mitochondrial respirasome ...TP53 Regulates Metabolic Genes / Cytoprotection by HMOX1 / respiratory chain complex IV assembly / mitochondrial respirasome assembly / respiratory chain complex IV / mitochondrial respiratory chain complex IV / regulation of oxidative phosphorylation / Respiratory electron transport / cytochrome-c oxidase / mitochondrial respirasome / oxidative phosphorylation / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / Mitochondrial protein degradation / electron transport coupled proton transport / ATP synthesis coupled electron transport / enzyme regulator activity / central nervous system development / mitochondrial inner membrane / oxidoreductase activity / copper ion binding / heme binding / mitochondrion / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Muramoto, K. / Ohta, K. / Shinzawa-Itoh, K. / Kanda, K. / Taniguchi, M. / Nabekura, H. / Yamashita, E. / Tsukihara, T. / Yoshikawa, S. | ||||||
![]() | ![]() Title: Bovine cytochrome c oxidase structures enable O2 reduction with minimization of reactive oxygens and provide a proton-pumping gate Authors: Muramoto, K. / Ohta, K. / Shinzawa-Itoh, K. / Kanda, K. / Taniguchi, M. / Nabekura, H. / Yamashita, E. / Tsukihara, T. / Yoshikawa, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 813.9 KB | Display | ![]() |
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PDB format | ![]() | 664.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 9.4 MB | Display | ![]() |
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Full document | ![]() | 9.9 MB | Display | |
Data in XML | ![]() | 196.2 KB | Display | |
Data in CIF | ![]() | 242.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ag2C ![]() 3ag3C ![]() 3ag4C ![]() 8ijnC ![]() 2eijS S: Starting model for refinement 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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2 | ![]()
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Unit cell |
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Components
-Cytochrome c oxidase subunit ... , 12 types, 24 molecules ANBOCPDQERFSGTHUIVKXLYMZ
#1: Protein | Mass: 57093.852 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Protein | Mass: 26068.404 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Protein | Mass: 29957.627 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #4: Protein | Mass: 17179.646 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #5: Protein | Mass: 12453.081 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #6: Protein | Mass: 10684.038 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #7: Protein | Mass: 9629.782 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #8: Protein | Mass: 10039.244 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #9: Protein | Mass: 8537.019 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #11: Protein | Mass: 6365.217 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #12: Protein/peptide | Mass: 5449.396 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #13: Protein/peptide | Mass: 4967.756 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Protein / Sugars , 2 types, 6 molecules JW![](data/chem/img/DMU.gif)
![](data/chem/img/DMU.gif)
#10: Protein | Mass: 6682.726 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #26: Sugar | ChemComp-DMU / |
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-Non-polymers , 15 types, 1421 molecules ![](data/chem/img/HEA.gif)
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![](data/chem/img/CU.gif)
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![](data/chem/img/NA.gif)
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![](data/chem/img/PSC.gif)
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![](data/chem/img/CDL.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/PEK.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CMO.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/TGL.gif)
![](data/chem/img/PGV.gif)
![](data/chem/img/CUA.gif)
![](data/chem/img/PSC.gif)
![](data/chem/img/CHD.gif)
![](data/chem/img/UNX.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/PEK.gif)
![](data/chem/img/HOH.gif)
#14: Chemical | ChemComp-HEA / #15: Chemical | #16: Chemical | #17: Chemical | #18: Chemical | #19: Chemical | ChemComp-TGL / #20: Chemical | ChemComp-PGV / ( #21: Chemical | #22: Chemical | #23: Chemical | ChemComp-CHD / #24: Chemical | #25: Chemical | ChemComp-CDL / #27: Chemical | #28: Chemical | ChemComp-PEK / ( #29: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.34 Å3/Da / Density % sol: 71.67 % |
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-Data collection
Diffraction | Mean temperature: 280 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Date: Nov 28, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→94.9 Å / Num. obs: 353208 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2EIJ Resolution: 2.2→40 Å
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Refinement step | Cycle: LAST / Resolution: 2.2→40 Å
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