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- PDB-2y69: Bovine heart cytochrome c oxidase re-refined with molecular oxygen -
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Open data
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Basic information
Entry | Database: PDB / ID: 2y69 | ||||||
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Title | Bovine heart cytochrome c oxidase re-refined with molecular oxygen | ||||||
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![]() | ELECTRON TRANSPORT / COMPLEX IV / PROTON PUMPS / MEMBRANE PROTEIN | ||||||
Function / homology | ![]() TP53 Regulates Metabolic Genes / Cytoprotection by HMOX1 / respiratory chain complex IV assembly / mitochondrial respirasome assembly / respiratory chain complex IV / : / regulation of oxidative phosphorylation / Respiratory electron transport / cytochrome-c oxidase / : ...TP53 Regulates Metabolic Genes / Cytoprotection by HMOX1 / respiratory chain complex IV assembly / mitochondrial respirasome assembly / respiratory chain complex IV / : / regulation of oxidative phosphorylation / Respiratory electron transport / cytochrome-c oxidase / : / 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 | ![]() ![]() | ||||||
![]() | Kaila, V.R.I. / Oksanen, E. / Goldman, A. / Verkhovsky, M.I. / Sundholm, D. / Wikstrom, M. | ||||||
![]() | ![]() Title: A Peroxide Bridge between Fe and Cu Ions in the O2 Reduction Site of Fully Oxidized Cytochrome C Oxidase Could Suppress the Proton Pump. Authors: Aoyama, H. / Muramoto, K. / Shinzawa-Itoh, K. / Hirata, K. / Yamashita, E. / Tsukihara, T. / Ogura, T. / Yoshikawa, S. | ||||||
History |
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Remark 0 | THIS ENTRY 2Y69 REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA (R3ABMSF) ...THIS ENTRY 2Y69 REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA (R3ABMSF) DETERMINED BY AUTHORS OF THE PDB ENTRY 3ABM: H.AOYAMA,K.MURAMOTO,K.SHINZAWA-ITOH,K.HIRATA,E.YAMASHITA, T.TSUKIHARA,T.OGURA,S.YOSHIKAWA |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 752 KB | Display | ![]() |
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PDB format | ![]() | 630.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.3 MB | Display | ![]() |
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Full document | ![]() | 4.4 MB | Display | |
Data in XML | ![]() | 148.7 KB | Display | |
Data in CIF | ![]() | 203.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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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 C OXIDASE SUBUNIT ... , 8 types, 16 molecules ANBOCPDQERFSHULY
#1: Protein | Mass: 57065.844 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Protein | Mass: 26040.393 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: 19602.609 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #5: Protein | Mass: 16758.156 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #6: Protein | Mass: 13852.807 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #8: Protein | Mass: 10170.439 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #12: Protein | Mass: 7342.661 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-CYTOCHROME C OXIDASE POLYPEPTIDE ... , 5 types, 10 molecules GTIVJWKXMZ
#7: Protein | Mass: 10899.382 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #9: Protein | Mass: 8626.179 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #10: Protein | Mass: 9076.522 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #11: Protein | Mass: 9077.439 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #13: Protein | Mass: 7650.059 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Sugars , 1 types, 2 molecules ![](data/chem/img/DMU.gif)
#23: Sugar |
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-Non-polymers , 10 types, 1074 molecules ![](data/chem/img/HEA.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/OXY.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CHD.gif)
![](data/chem/img/CUA.gif)
![](data/chem/img/PEK.gif)
![](data/chem/img/PGV.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/OXY.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CHD.gif)
![](data/chem/img/CUA.gif)
![](data/chem/img/PEK.gif)
![](data/chem/img/PGV.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
#14: Chemical | ChemComp-HEA / #15: Chemical | #16: Chemical | #17: Chemical | #18: Chemical | ChemComp-CHD / #19: Chemical | #20: Chemical | #21: Chemical | ChemComp-PGV / ( #22: Chemical | #24: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.75 Å3/Da / Density % sol: 67.17 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 3ABM |
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-Data collection
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | Biso Wilson estimate: 0 Å2 |
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Processing
Software | Name: REFMAC / Version: 5.5.0066 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS ENTRY REFLECTS AN ALTERNATIVE MODELING OF X-RAY DATA R3ABMSF.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.538 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→64.15 Å
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Refine LS restraints |
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