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- PDB-5uvp: Kaposi's Sarcoma Herpesvirus Protease in Complex with Allosteric ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5uvp | ||||||
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Title | Kaposi's Sarcoma Herpesvirus Protease in Complex with Allosteric Inhibitor | ||||||
![]() | ORF 17 | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / Serine Hydrolase / Viral Protein / Capsid Maturation / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | ![]() assemblin / viral release from host cell / host cell cytoplasm / serine-type endopeptidase activity / host cell nucleus / proteolysis / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Acker, T.M. / Gable, J. / Bohn, M.-F. / Craik, C.S. | ||||||
![]() | ![]() Title: Kaposi's Sarcoma Herpesvirus Protease in Complex with Allosteric Inhibitor Authors: Acker, T.M. / Craik, C.S. / Bohn, M.-F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 149.8 KB | Display | ![]() |
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PDB format | ![]() | 119.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 19.4 KB | Display | |
Data in CIF | ![]() | 26.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ur3C ![]() 5uteC ![]() 5utnC ![]() 5uv3C ![]() 3njqS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 21193.111 Da / Num. of mol.: 2 / Fragment: residues 23-215 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.12 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1M Sodium acetate pH 5.5, 0.8M NaH2PO4/1.2M K2HPO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 17, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→73.103 Å / Num. obs: 27625 / % possible obs: 100 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.174 / Net I/σ(I): 6.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3NJQ Resolution: 1.94→73.103 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.77 / Stereochemistry target values: ML
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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: 152.68 Å2 / Biso mean: 43.2159 Å2 / Biso min: 18.35 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.94→73.103 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: 14
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