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- PDB-6t5d: 3C-like protease from Southampton virus complexed with FMOPL000014a. -
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Open data
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Basic information
Entry | Database: PDB / ID: 6t5d | ||||||
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Title | 3C-like protease from Southampton virus complexed with FMOPL000014a. | ||||||
![]() | (Genome polyprotein) x 2 | ||||||
![]() | HYDROLASE / Viral protease. | ||||||
Function / homology | ![]() calicivirin / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / RNA helicase activity / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / proteolysis ...calicivirin / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / RNA helicase activity / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / ATP binding Similarity search - Function | ||||||
Biological species | Southampton virus | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Guo, J. / Cooper, J.B. | ||||||
![]() | ![]() Title: In crystallo-screening for discovery of human norovirus 3C-like protease inhibitors. Authors: Guo, J. / Douangamath, A. / Song, W. / Coker, A.R. / Chan, A.W.E. / Wood, S.P. / Cooper, J.B. / Resnick, E. / London, N. / Delft, F.V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 166.1 KB | Display | ![]() |
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PDB format | ![]() | 130.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 539.6 KB | Display | ![]() |
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Full document | ![]() | 542.2 KB | Display | |
Data in XML | ![]() | 19.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6t1qSC ![]() 6t2iC ![]() 6t2xC ![]() 6t3gC ![]() 6t49C ![]() 6t4eC ![]() 6t4sC ![]() 6t5rC ![]() 6t6wC ![]() 6t71C ![]() 6t82C ![]() 6t8rC ![]() 6t8tC ![]() 6talC ![]() 6tawC ![]() 6tboC ![]() 6tbpC ![]() 6tc1C ![]() 6tcfC ![]() 6tglC 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 on special symmetry positions |
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Components
#1: Protein | Mass: 18387.350 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: Q04544, nucleoside-triphosphate phosphatase, calicivirin, RNA-directed RNA polymerase |
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#2: Protein | Mass: 18387.350 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: Q04544, nucleoside-triphosphate phosphatase, calicivirin, RNA-directed RNA polymerase |
#3: Chemical | ChemComp-MJW / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.15 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.1 Details: Protein concentration 4 mg/ml. 0.2 M ammonium citrate and 12% (v/v) PEG3350. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 5, 2016 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.92819 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.42→61.07 Å / Num. obs: 60967 / % possible obs: 96.4 % / Redundancy: 2.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.034 / Rpim(I) all: 0.023 / Rrim(I) all: 0.042 / Net I/σ(I): 15 / Num. measured all: 179818 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6t1q Resolution: 1.42→61.07 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.905 / SU ML: 0.049 / SU R Cruickshank DPI: 0.0608 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.061 / ESU R Free: 0.065 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS ANISOTROPIC U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 147.8 Å2 / Biso mean: 26.087 Å2 / Biso min: 9.67 Å2
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Refinement step | Cycle: final / Resolution: 1.42→61.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.42→1.457 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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