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- PDB-4nvl: Predicting protein conformational response in prospective ligand ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4nvl | ||||||
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Title | Predicting protein conformational response in prospective ligand discovery. | ||||||
![]() | Cytochrome c peroxidase | ||||||
![]() | OXIDOREDUCTASE / Model system / flexibility / dynamic / loop / side-chains / energy penalty / occupancy / Boltzmann weights / flexible 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. / Fraser, J.S. | ||||||
![]() | ![]() 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 | ![]() | 159.8 KB | Display | ![]() |
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PDB format | ![]() | 126.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 830 KB | Display | ![]() |
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Full document | ![]() | 835.2 KB | Display | |
Data in XML | ![]() | 19 KB | Display | |
Data in CIF | ![]() | 29.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4nvaC ![]() 4nvbC ![]() 4nvcC ![]() 4nvdC ![]() 4nveC ![]() 4nvfC ![]() 4nvgC ![]() 4nvhC ![]() 4nviC ![]() 4nvjC ![]() 4nvkC ![]() 4nvmC ![]() 4nvnC ![]() 4nvoC ![]() 4oq7C 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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Unit cell |
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Components
#1: Protein | Mass: 32928.582 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 72-362 / Mutation: P190G, W191G, DELETIONS G192-A193 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: RM11-1A / Gene: CCP1 CCP CPO YKR066C, SCRG_04081 / Production host: ![]() ![]() | ||||
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#2: Chemical | ChemComp-HEM / | ||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.41 % |
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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, vapor diffusion, hanging drop, temperature 283K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 18, 2012 |
Radiation | Monochromator: KOHZU DUAL DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11587 Å / Relative weight: 1 |
Reflection | Resolution: 1.43→32.6 Å / Num. all: 71072 / Num. obs: 71072 / % possible obs: 98.1 % / Observed criterion σ(F): 1.35 / Observed criterion σ(I): 2.2 / Redundancy: 3.9 % / Biso Wilson estimate: 14.1 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 21.3 |
Reflection shell | Resolution: 1.43→1.47 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 2.2 / Num. unique all: 4463 / % possible all: 85.1 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.012 Å2 / ksol: 0.336 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 57.63 Å2 / Biso mean: 16.5433 Å2 / Biso min: 6.27 Å2
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Refinement step | Cycle: LAST / Resolution: 1.432→32.6 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26
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