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- PDB-6vmz: Crystal Structure of a H5N1 influenza virus hemagglutinin with CBS1117 -
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Open data
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Basic information
Entry | Database: PDB / ID: 6vmz | ||||||
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Title | Crystal Structure of a H5N1 influenza virus hemagglutinin with CBS1117 | ||||||
![]() | (Hemagglutinin) x 2 | ||||||
![]() | VIRAL PROTEIN / Influenza / H5 / CBS1117 | ||||||
Function / homology | ![]() clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / 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: Structure of avian influenza hemagglutinin in complex with a small molecule entry inhibitor. Authors: Antanasijevic, A. / Durst, M.A. / Cheng, H. / Gaisina, I.N. / Perez, J.T. / Manicassamy, B. / Rong, L. / 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 | ![]() | 314.8 KB | Display | ![]() |
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PDB format | ![]() | 252.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 425.3 KB | Display | ![]() |
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Full document | ![]() | 432.5 KB | Display | |
Data in XML | ![]() | 3.2 KB | Display | |
Data in CIF | ![]() | 19.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2fkoS 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 domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / Refine code: _
NCS ensembles :
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Components
#1: Protein | Mass: 37948.020 Da / Num. of mol.: 3 / Fragment: N-terminal domain (UNP residues 17-337) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: A/chicken/Vietnam/4/2003(H5N1) / Gene: HA / Production host: ![]() #2: Protein | Mass: 20881.104 Da / Num. of mol.: 3 / Fragment: C-terminal domain (UNP residues 347-521) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: A/chicken/Vietnam/30/2003(H5N1) / Gene: HA / Production host: ![]() #3: Sugar | ChemComp-NAG / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.24 Å3/Da / Density % sol: 56.63 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 100 mM Tris, pH 8.5, 20% PEG6000, 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: Feb 24, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→29.47 Å / Num. obs: 110799 / % possible obs: 94.1 % / Redundancy: 5.49 % / CC1/2: 0.998 / Rmerge(I) obs: 0.084 / Rrim(I) all: 0.092 / Net I/σ(I): 12.28 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 5.35 % / Rmerge(I) obs: 0.645 / Mean I/σ(I) obs: 2.34 / Num. unique obs: 17093 / CC1/2: 0.755 / Rrim(I) all: 0.714 / % possible all: 91.2 |
-Phasing
Phasing | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2FKO Resolution: 2.2→29.47 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.928 / SU B: 7.141 / SU ML: 0.167 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.224 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 147.13 Å2 / Biso mean: 49.644 Å2 / Biso min: 18.34 Å2
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Refinement step | Cycle: final / Resolution: 2.2→29.47 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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