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- PDB-6cf5: Crystal structure of the A/Viet Nam/1203/2004(H5N1) influenza vir... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6cf5 | |||||||||
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Title | Crystal structure of the A/Viet Nam/1203/2004(H5N1) influenza virus hemagglutinin in complex with small molecule N-Cyclohexyltaurine | |||||||||
![]() | (Hemagglutinin) x 2 | |||||||||
![]() | VIRAL PROTEIN / Glycoprotein / Ectodomain / N-glycosylation | |||||||||
Function / homology | ![]() viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / apical plasma membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane ...viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / apical plasma membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / identical protein binding / membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Wilson, I.A. / Kadam, R.U. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: A small-molecule fragment that emulates binding of receptor and broadly neutralizing antibodies to influenza A hemagglutinin. Authors: Kadam, R.U. / Wilson, I.A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 348.9 KB | Display | ![]() |
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PDB format | ![]() | 277.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 69.3 KB | Display | |
Data in CIF | ![]() | 99.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6cexC ![]() 4fqiS 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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Unit cell |
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Components
-Protein , 2 types, 6 molecules ACEBDF
#1: Protein | Mass: 37948.020 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: A/Viet Nam/1203/2004(H5N1) / Gene: HA / Production host: ![]() #2: Protein | Mass: 20414.504 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: A/Viet Nam/1203/2004(H5N1) / Gene: HA / Production host: ![]() |
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-Sugars , 2 types, 6 molecules ![](data/chem/img/NAG.gif)
#3: Polysaccharide | #5: Sugar | |
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-Non-polymers , 4 types, 1344 molecules ![](data/chem/img/NHE.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #6: Chemical | ChemComp-PEG / #7: Chemical | ChemComp-GOL / #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 59.94 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 100 mM of CHES, pH 9.5 and 40% v/v PEG600, 20 degree celsiu |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 22, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→50 Å / Num. obs: 131851 / % possible obs: 98.4 % / Redundancy: 3.5 % / Biso Wilson estimate: 24 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.02 / Rsym value: 0.04 / Net I/σ(I): 29.3 |
Reflection shell | Resolution: 2.04→2.08 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 6.9 / Num. unique obs: 6021 / CC1/2: 0.97 / Rpim(I) all: 0.08 / Rsym value: 0.16 / % possible all: 88.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4FQI Resolution: 2.04→37.583 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.27
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.04→37.583 Å
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Refine LS restraints |
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LS refinement shell |
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