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Open data
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Basic information
Entry | Database: PDB / ID: 3zp1 | |||||||||
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Title | INFLUENZA VIRUS (VN1194) H5 HA with LSTc | |||||||||
![]() | (HAEMAGGLUTININ) x 2 | |||||||||
![]() | VIRAL PROTEIN | |||||||||
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 | ![]() ![]() | |||||||||
![]() | Liu, J. / Stevens, D.J. / Gamblin, S.J. / Skehel, J.J. | |||||||||
![]() | ![]() Title: Changes in the Hemagglutinin of H5N1 Viruses During Human Infection - Influence on Receptor Binding. Authors: Crusat, M. / Liu, J. / Palma, A.S. / Childs, R.A. / Liu, Y. / Wharton, S.A. / Lin, Y.P. / Coombs, P.J. / Martin, S.R. / Matrosovich, M. / Chen, Z. / Stevens, D.J. / Hien, V.M. / Thanh, T.T. ...Authors: Crusat, M. / Liu, J. / Palma, A.S. / Childs, R.A. / Liu, Y. / Wharton, S.A. / Lin, Y.P. / Coombs, P.J. / Martin, S.R. / Matrosovich, M. / Chen, Z. / Stevens, D.J. / Hien, V.M. / Thanh, T.T. / Nhu, L.N.T. / Nguyet, L.A. / Ha, D.Q. / van Doorn, H.R. / Hien, T.T. / Conradt, H.S. / Kiso, M. / Gamblin, S.J. / Chai, W. / Skehel, J.J. / Hay, A.J. / Farrar, J. / De Jong, M.D. / Feizi, T. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 201.5 KB | Display | ![]() |
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PDB format | ![]() | 165.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 790.3 KB | Display | ![]() |
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Full document | ![]() | 802.2 KB | Display | |
Data in XML | ![]() | 21.9 KB | Display | |
Data in CIF | ![]() | 30.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3zp0C ![]() 3zp2C ![]() 3zp3C ![]() 3zp6C ![]() 3zpaC ![]() 3zpbC 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
#1: Protein | Mass: 37034.934 Da / Num. of mol.: 1 Fragment: HA1 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES 17-342 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Description: THE NATIONAL INSTITUTE FOR BIOLOGICAL STANDARDS AND CONTROL (NIBSC) Variant: VN/1194/04/NIBRG14 VACCINE STRAIN / Organ (production host): EGG / Production host: ![]() ![]() |
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#2: Protein | Mass: 19097.990 Da / Num. of mol.: 1 Fragment: HA2 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES 347-512 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Description: THE NATIONAL INSTITUTE FOR BIOLOGICAL STANDARDS AND CONTROL (NIBSC) Variant: VN/1194/04/NIBRG14 VACCINE STRAIN / Organ (production host): EGG / Production host: ![]() ![]() |
#3: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-2)-beta-D-galactopyranose Source method: isolated from a genetically manipulated source |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.93 Å3/Da / Density % sol: 68.69 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() ![]() ![]() |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9715 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. obs: 24984 / % possible obs: 99.6 % / Observed criterion σ(I): 2.3 / Redundancy: 10.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 18.2 |
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Processing
Software | Name: REFMAC / Version: 5.5.0088 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.899 / SU B: 24.938 / SU ML: 0.238 / Cross valid method: THROUGHOUT / ESU R: 0.473 / ESU R Free: 0.329 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.6→30 Å
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Refine LS restraints |
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