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- PDB-6pd5: Crystal Structure of a H5N1 influenza virus hemagglutinin at pH 6.5 -
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Open data
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Basic information
Entry | Database: PDB / ID: 6pd5 | ||||||
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Title | Crystal Structure of a H5N1 influenza virus hemagglutinin at pH 6.5 | ||||||
![]() | Hemagglutinin | ||||||
![]() | VIRAL PROTEIN / Influenza / H5 | ||||||
Function / homology | ![]() 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 Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Antanasijevic, A. / Durst, M.A. / Lavie, A. / Caffrey, M. | ||||||
![]() | ![]() Title: Identification of a pH sensor in Influenza hemagglutinin using X-ray crystallography. Authors: Antanasijevic, A. / Durst, M.A. / Lavie, A. / Caffrey, 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 | ![]() | 121.1 KB | Display | ![]() |
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PDB format | ![]() | 91.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 480.8 KB | Display | ![]() |
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Full document | ![]() | 489.3 KB | Display | |
Data in XML | ![]() | 21.4 KB | Display | |
Data in CIF | ![]() | 29.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6pcxC ![]() 6pd3C ![]() 6pd6C ![]() 2fk0S 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: 59893.277 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: A/chicken/Vietnam/4/2003(H5N1) / Gene: HA / Production host: ![]() | ||||||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Sugar | ChemComp-NAG / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.94 Å3/Da / Density % sol: 68.81 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100 mM cacodylate, pH 6.5, 200 mM sodium chloride, 2 M ammonium sulfate, 10% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 3, 2016 |
Radiation | Monochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.39→30 Å / Num. obs: 37825 / % possible obs: 99.5 % / Redundancy: 9.14 % / CC1/2: 0.997 / Rrim(I) all: 0.163 / Net I/σ(I): 12.29 |
Reflection shell | Resolution: 2.39→2.52 Å / Redundancy: 8.65 % / Mean I/σ(I) obs: 2.57 / Num. unique obs: 5929 / CC1/2: 0.857 / Rrim(I) all: 1.764 / % possible all: 98.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2FK0 Resolution: 2.39→29.35 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.929 / SU B: 16.492 / SU ML: 0.301 / SU R Cruickshank DPI: 0.246 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.246 / ESU R Free: 0.219 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 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: 192.98 Å2 / Biso mean: 58.252 Å2 / Biso min: 28.4 Å2
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Refinement step | Cycle: final / Resolution: 2.39→29.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.39→2.452 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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