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- PDB-6tsd: Crystal structure of human coxsackievirus A24v in complex with pe... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6tsd | ||||||||||||
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Title | Crystal structure of human coxsackievirus A24v in complex with pentavalent inhibitor ME0752 | ||||||||||||
![]() | (Capsid protein ...) x 4 | ||||||||||||
![]() | VIRUS / human Coxsackievirus A24v / starfish-like inhibitor / pentavelent | ||||||||||||
Function / homology | ![]() picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase ...picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / symbiont-mediated suppression of host gene expression / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / metal ion binding Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Zocher, G. / Stehle, T. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Pentavalent Sialic Acid Conjugates Block Coxsackievirus A24 Variant and Human Adenovirus Type 37-Viruses That Cause Highly Contagious Eye Infections. Authors: Johansson, E. / Caraballo, R. / Mistry, N. / Zocher, G. / Qian, W. / Andersson, C.D. / Hurdiss, D.L. / Chandra, N. / Thompson, R. / Frangsmyr, L. / Stehle, T. / Arnberg, N. / Elofsson, M. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 215.2 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 845.9 KB | Display | ![]() |
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Full document | ![]() | 848.5 KB | Display | |
Data in XML | ![]() | 18.5 KB | Display | |
Data in CIF | ![]() | 32.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4q4wS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
-Capsid protein ... , 4 types, 4 molecules 111222333444
#1: Protein | Mass: 34378.371 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Protein | Mass: 29817.412 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#3: Protein | Mass: 26637.746 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#4: Protein | Mass: 7319.045 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Sugars , 1 types, 1 molecules ![](data/chem/img/SIA.gif)
#5: Sugar | ChemComp-SIA / |
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-Non-polymers , 6 types, 834 molecules ![](data/chem/img/HEZ.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | ChemComp-HEZ / #7: Chemical | ChemComp-CL / #8: Chemical | ChemComp-NA / | #9: Chemical | ChemComp-CA / #10: Chemical | ChemComp-MG / | #11: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 200 mM Magnesium chloride, 3.4 M 1,6-Hexanediol, 100 mM HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 14, 2016 |
Radiation | Monochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→50 Å / Num. obs: 14074225 / % possible obs: 99.9 % / Redundancy: 7.71 % / CC1/2: 0.993 / Net I/σ(I): 8.18 |
Reflection shell | Resolution: 1.81→1.92 Å / Num. unique obs: 2244009 / CC1/2: 0.679 / % possible all: 99.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4Q4w Resolution: 1.81→49.955 Å / Cor.coef. Fo:Fc: 0.97 / SU B: 1.889 / SU ML: 0.054 / Cross valid method: NONE / ESU R: 0.018 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.473 Å2
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Refinement step | Cycle: LAST / Resolution: 1.81→49.955 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Num. reflection Rfree: _ / Total num. of bins used: 20
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