[English] 日本語
![](img/lk-miru.gif)
- PDB-7ypy: Bovine heart cytochrome c oxidase in fully oxidized state at 1.5 ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7ypy | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Bovine heart cytochrome c oxidase in fully oxidized state at 1.5 angstrom resolution | |||||||||
![]() | (Cytochrome c oxidase subunit ...) x 14 | |||||||||
![]() | OXIDOREDUCTASE / Respiratory enzyme / Membrane protein / Hemeprotein / Protein complex | |||||||||
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 | ![]() ![]() ![]() | |||||||||
![]() | Shimada, A. / Tsukihara, T. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: The Mg2+-containing water cluster of mammalian cytochrome c oxidase collects four pumping proton equivalents in each catalytic cycle. Authors: Yano, N. / Muramoto, K. / Shimada, A. / Shinzawa-Itoh, K. / Tsukihara, T. / Yoshikawa, S. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 1.5 MB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 1.3 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 14.4 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 14.6 MB | Display | |
Data in XML | ![]() | 203.1 KB | Display | |
Data in CIF | ![]() | 268.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5b1aSC ![]() 5b1bC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
-Cytochrome c oxidase subunit ... , 14 types, 26 molecules ANBOCPDQERFSGHUIVJWKXLYMZT
#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.: 1 / 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) ![]() ![]() #10: Protein | Mass: 6682.726 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) ![]() ![]() #14: Protein | | Mass: 9549.802 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
---|
-Sugars , 1 types, 26 molecules ![](data/chem/img/DMU.gif)
#23: Sugar | ChemComp-DMU / |
---|
-Non-polymers , 16 types, 2945 molecules ![](data/chem/img/HEA.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PER.gif)
![](data/chem/img/PGV.gif)
![](data/chem/img/TGL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CUA.gif)
![](data/chem/img/CHD.gif)
![](data/chem/img/PSC.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/PEK.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PER.gif)
![](data/chem/img/PGV.gif)
![](data/chem/img/TGL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CUA.gif)
![](data/chem/img/CHD.gif)
![](data/chem/img/PSC.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/PEK.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
#15: Chemical | ChemComp-HEA / #16: Chemical | #17: Chemical | #18: Chemical | #19: Chemical | #20: Chemical | ChemComp-PGV / ( #21: Chemical | ChemComp-TGL / #22: Chemical | ChemComp-EDO / #24: Chemical | #25: Chemical | ChemComp-CHD / #26: Chemical | #27: Chemical | ChemComp-CDL / #28: Chemical | ChemComp-PEK / ( #29: Chemical | #30: Chemical | #31: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 4.03 Å3/Da / Density % sol: 69.49 % / Description: tetragonal plate |
---|---|
Crystal grow | Temperature: 277 K / Method: batch mode / pH: 6.8 / Details: Sodium phosphate buffer, PEG 4000 |
-Data collection
Diffraction | Mean temperature: 50 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Apr 23, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→200 Å / Num. obs: 1041861 / % possible obs: 100 % / Redundancy: 14.9 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 32.7 |
Reflection shell | Resolution: 1.5→1.52 Å / Redundancy: 14.8 % / Mean I/σ(I) obs: 3.9 / Num. unique obs: 34593 / Rpim(I) all: 0.296 / % possible all: 100 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5B1A Resolution: 1.5→39.955 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 19.42 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→39.955 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|