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Open data
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Basic information
Entry | Database: PDB / ID: 5u5y | ||||||
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Title | CcP gateless cavity | ||||||
![]() | Peroxidase | ||||||
![]() | OXIDOREDUCTASE / Model system / Cytochrome c Peroxidase / GIST / water / desolvation / docking / ligand binding | ||||||
Function / homology | ![]() cytochrome-c peroxidase activity / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / response to reactive oxygen species / hydrogen peroxide catabolic process / cellular response to oxidative stress / mitochondrial matrix / heme binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Fischer, M. / Shoichet, B.K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Testing inhomogeneous solvation theory in structure-based ligand discovery. Authors: Balius, T.E. / Fischer, M. / Stein, R.M. / Adler, T.B. / Nguyen, C.N. / Cruz, A. / Gilson, M.K. / Kurtzman, T. / Shoichet, B.K. #1: ![]() Title: Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery. Authors: Fischer, M. / Coleman, R.G. / Fraser, J.S. / Shoichet, B.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 144.4 KB | Display | ![]() |
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PDB format | ![]() | 110.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5u5uC ![]() 5u5vC ![]() 5u5wC ![]() 5u5xC ![]() 5u5zC ![]() 5u60C ![]() 5u61C ![]() 5ug2C 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: 32928.582 Da / Num. of mol.: 1 / Mutation: P190G, W191G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: RM11-1a / Gene: SCRG_04081 / Production host: ![]() ![]() References: UniProt: B3LRE1, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-7W4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 59.7 % / Mosaicity: 0 ° |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6 Details: Compound soaked into crystal grown in equal volume of 500mM MES buffer (pH 6.0) and 25% MPD |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 13, 2016 | ||||||||||||||||||
Radiation | Monochromator: KOHZU DUAL DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 1.1158 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 1.3→74.66 Å / Num. obs: 93112 / % possible obs: 91.6 % / Redundancy: 11.3 % / Biso Wilson estimate: 13.41 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.018 / Rrim(I) all: 0.063 / Net I/σ(I): 16.6 / Num. measured all: 1054450 / Scaling rejects: 1146 | ||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 56.29 Å2 / Biso mean: 19.5476 Å2 / Biso min: 10.21 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.3→46.223 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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