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- PDB-1aej: SPECIFICITY OF LIGAND BINDING TO A BURIED POLAR CAVITY AT THE ACT... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1aej | ||||||
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Title | SPECIFICITY OF LIGAND BINDING TO A BURIED POLAR CAVITY AT THE ACTIVE SITE OF CYTOCHROME C PEROXIDASE (1-VINYLIMIDAZOLE) | ||||||
![]() | CYTOCHROME C PEROXIDASE | ||||||
![]() | OXIDOREDUCTASE / PEROXIDASE / TRANSIT PEPTIDE | ||||||
Function / homology | ![]() cytochrome-c peroxidase / cytochrome-c peroxidase activity / response to reactive oxygen species / hydrogen peroxide catabolic process / peroxidase activity / mitochondrial intermembrane space / cellular response to oxidative stress / mitochondrial matrix / heme binding / mitochondrion / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Musah, R.A. / Jensen, G.M. / Fitzgerald, M.M. / Mcree, D.E. / Goodin, D.B. | ||||||
![]() | ![]() Title: Artificial protein cavities as specific ligand-binding templates: characterization of an engineered heterocyclic cation-binding site that preserves the evolved specificity of the parent protein. Authors: Musah, R.A. / Jensen, G.M. / Bunte, S.W. / Rosenfeld, R.J. / Goodin, D.B. #1: ![]() Title: Small Molecule Binding to an Artificially Created Cavity at the Active Site of Cytochrome C Peroxidase Authors: Fitzgerald, M.M. / Churchill, M.J. / Mcree, D.E. / Goodin, D.B. #2: ![]() Title: The Asp-His-Fe Triad of Cytochrome C Peroxidase Controls the Reduction Potential, Electronic Structure, and Coupling of the Tryptophan Free Radical to the Heme Authors: Goodin, D.B. / Mcree, D.E. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 86 KB | Display | ![]() |
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PDB format | ![]() | 64.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1aebC ![]() 1aedC ![]() 1aeeC ![]() 1aefC ![]() 1aegC ![]() 1aehC ![]() 1aekC ![]() 1aemC ![]() 1aenC ![]() 1aeoC ![]() 1aeqC ![]() 1aa4S 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 33459.242 Da / Num. of mol.: 1 / Mutation: W191G Source method: isolated from a genetically manipulated source Details: CRYSTAL FORM BY Source: (gene. exp.) ![]() ![]() Cell line: BL21 / Cellular location: MITOCHONDRIA / Gene: CCP / Organelle: MITOCHONDRIA / Plasmid: PT7CCP / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Gene (production host): CCP (MKT) / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-NVI / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61 % | ||||||||||||||||||||
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Crystal grow | pH: 6 Details: 20% MPD, 40 MM PHOSPHATE PH 6.0. A SINGLE CRYSTAL OF W191G WAS SOAKED IN 50MM 1-VINYLIMIDAZOLE, 5MM ETHANOL, IN 40% MPD AND 60 MM PHOSPHATE AT PH 4.5. | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion, sitting drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 290 K |
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Diffraction source | Source: ![]() |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Jun 1, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→15 Å / Num. obs: 23913 / % possible obs: 84 % / Observed criterion σ(I): 0 / Redundancy: 1.85 % / Rmerge(I) obs: 0.087 / Rsym value: 0.085 / Net I/σ(I): 8.44 |
Reflection shell | Resolution: 2.01→2.14 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 1.1 / Rsym value: 0.77 / % possible all: 71 |
Reflection | *PLUS Num. obs: 22158 / Rmerge(I) obs: 0.085 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1AA4 Resolution: 2.1→7 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.5 / σ(F): 0 /
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Refinement step | Cycle: LAST / Resolution: 2.1→7 Å
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