+Open data
-Basic information
Entry | Database: PDB / ID: 2orl | ||||||
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Title | Solution structure of the cytochrome c- para-aminophenol adduct | ||||||
Components | Cytochrome c iso-1 | ||||||
Keywords | ELECTRON TRANSPORT / protein-ligand adduct | ||||||
Function / homology | Function and homology information Pyroptosis / Release of apoptotic factors from the mitochondria / Detoxification of Reactive Oxygen Species / Respiratory electron transport / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / mitochondrial intermembrane space / electron transfer activity / heme binding ...Pyroptosis / Release of apoptotic factors from the mitochondria / Detoxification of Reactive Oxygen Species / Respiratory electron transport / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / mitochondrial intermembrane space / electron transfer activity / heme binding / mitochondrion / metal ion binding Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | SOLUTION NMR / combined docking, simulated annealing with NMR restraints | ||||||
Authors | Assfalg, M. / Bertini, I. / Del Conte, R. / Giachetti, A. / Turano, P. | ||||||
Citation | Journal: Biochemistry / Year: 2007 Title: Cytochrome c and organic molecules: solution structure of the p-aminophenol adduct. Authors: Assfalg, M. / Bertini, I. / Del Conte, R. / Giachetti, A. / Turano, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2orl.cif.gz | 866.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2orl.ent.gz | 749.4 KB | Display | PDB format |
PDBx/mmJSON format | 2orl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/or/2orl ftp://data.pdbj.org/pub/pdb/validation_reports/or/2orl | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 12071.796 Da / Num. of mol.: 1 / Mutation: C102T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: CYC1 / Production host: Escherichia coli (E. coli) / References: UniProt: P00044 |
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#2: Chemical | ChemComp-HEC / |
#3: Chemical | ChemComp-4NL / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Type: 3D 15N-separated NOESY |
-Sample preparation
Details | Contents: 2-3mM Cytochrome c U-15N, 50mM phosphate buffer, pH 7.0, 90% H2O, 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 50 mM phosphate buffer / pH: 7.0 / Pressure: 1 atm / Temperature: 303 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz |
-Processing
NMR software |
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Refinement | Method: combined docking, simulated annealing with NMR restraints Software ordinal: 1 Details: four intermolecular NOEs were used together with intra-protein NOEs and angle constraints | |||||||||||||||
NMR representative | Selection criteria: lowest energy | |||||||||||||||
NMR ensemble | Conformer selection criteria: structure with the lowest interaction energy Conformers calculated total number: 100 / Conformers submitted total number: 25 |