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- PDB-4nvk: Predicting protein conformational response in prospective ligand ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4nvk | ||||||
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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 | ![]() | 154.7 KB | Display | ![]() |
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PDB format | ![]() | 121 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4nvaC ![]() 4nvbC ![]() 4nvcC ![]() 4nvdC ![]() 4nveC ![]() 4nvfC ![]() 4nvgC ![]() 4nvhC ![]() 4nviC ![]() 4nvjC ![]() 4nvlC ![]() 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 | ChemComp-2NY / |
#4: Chemical | ChemComp-PO4 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.54 % |
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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: 1.56→30.9 Å / Num. all: 53815 / Num. obs: 53815 / % possible obs: 99.8 % / Observed criterion σ(F): 1.34 / Observed criterion σ(I): 2.1 / Redundancy: 4.3 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 1.56→1.6 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.566 / Mean I/σ(I) obs: 2.1 / Num. unique all: 3925 / % possible all: 99.8 |
-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: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 62.79 Å2 / Biso mean: 23.0991 Å2 / Biso min: 10.79 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.56→30.9 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: 19
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