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- PDB-5jqb: Crystal structure of Ebola glycoprotein in complex with ibuprofen -
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Open data
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Basic information
Entry | Database: PDB / ID: 5jqb | |||||||||
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Title | Crystal structure of Ebola glycoprotein in complex with ibuprofen | |||||||||
![]() | (Envelope glycoprotein ...) x 2 | |||||||||
![]() | VIRAL PROTEIN / Ebola virus / Filoviridae / envelope glycoprotein / protein inhibitor complex / ibuprofen / toremifene | |||||||||
Function / homology | ![]() host cell endoplasmic reticulum / viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / suppression by virus of host tetherin activity / host cell cytoplasm / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / membrane raft / fusion of virus membrane with host endosome membrane / viral envelope ...host cell endoplasmic reticulum / viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / suppression by virus of host tetherin activity / host cell cytoplasm / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / membrane raft / fusion of virus membrane with host endosome membrane / viral envelope / lipid binding / host cell plasma membrane / virion membrane / extracellular region / identical protein binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() Zaire 1976 | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Zhao, Y. / Ren, J. / Stuart, D.I. | |||||||||
![]() | ![]() Title: Toremifene interacts with and destabilizes the Ebola virus glycoprotein. Authors: Zhao, Y. / Ren, J. / Harlos, K. / Jones, D.M. / Zeltina, A. / Bowden, T.A. / Padilla-Parra, S. / Fry, E.E. / Stuart, D.I. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 173.3 KB | Display | ![]() |
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PDB format | ![]() | 135.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 812 KB | Display | ![]() |
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Full document | ![]() | 815.6 KB | Display | |
Data in XML | ![]() | 17.2 KB | Display | |
Data in CIF | ![]() | 23 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5jq3SC ![]() 5jq7C 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
-Envelope glycoprotein ... , 2 types, 2 molecules AB
#1: Protein | Mass: 36302.719 Da / Num. of mol.: 1 / Mutation: T42A,T42A,T42A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 18989.391 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Sugars , 2 types, 5 molecules ![](data/chem/img/NAG.gif)
#3: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#4: Sugar | ChemComp-NAG / |
-Non-polymers , 3 types, 79 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/IBP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/IBP.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-IBP / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.49 Å3/Da / Density % sol: 64.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 9% (w/v) PEG 6000 and 0.1 M Sodium citrate tribasic dihydrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 26, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.68→82.84 Å / Num. obs: 21842 / % possible obs: 99.9 % / Redundancy: 9.8 % / Rmerge(I) obs: 0.129 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 2.68→2.75 Å / Redundancy: 8.3 % / Mean I/σ(I) obs: 1.5 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5JQ3 Resolution: 2.68→82.84 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.923 / SU B: 20.159 / SU ML: 0.202 / Cross valid method: THROUGHOUT / ESU R: 0.35 / ESU R Free: 0.253 / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 73.22 Å2
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Refinement step | Cycle: LAST / Resolution: 2.68→82.84 Å
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Refine LS restraints |
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