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- PDB-3znk: H5 Haemagglutinin in Complex with 6-O-Sulfo-2,3-Sialyllactosamine... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3znk | |||||||||
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Title | H5 Haemagglutinin in Complex with 6-O-Sulfo-2,3-Sialyllactosamine (Sulfated 3'SLN) | |||||||||
![]() | (HAEMAGGLUTININ) x 2 | |||||||||
![]() | VIRAL PROTEIN / SIALIC ACID / GLYCOPROTEIN / VIRUS RECEPTOR / SULFATED SIALOSIDE / FUCOSYLATED SIALOSIDE / SULFATION / FUCOSYLATION / AVIAN FLU / SIALYLLACTOSAMINE / LEWIS X | |||||||||
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 / virion membrane / membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Xiong, X. / Tuzikov, A. / Coombs, P. / Martin, S.R. / Walker, P.A. / Gamblin, S.J. / Bovin, N. / Skehel, J.J. | |||||||||
![]() | ![]() Title: Recognition of Sulphated and Fucosylated Receptor Sialosides by A/Vietnam/1194/2004 (H5N1) Influenza Virus. Authors: Xiong, X. / Tuzikov, A. / Coombs, P. / Martin, S. / Walker, P.A. / Gamblin, S.J. / Bovin, N. / Skehel, J.J. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 596.5 KB | Display | ![]() |
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PDB format | ![]() | 499.5 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 | ![]() | 55.1 KB | Display | |
Data in CIF | ![]() | 73.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3znlC ![]() 3znmC ![]() 2ibxS C: citing same article ( 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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Components
-Protein , 2 types, 6 molecules ACEBDF
#1: Protein | Mass: 36950.766 Da / Num. of mol.: 3 Fragment: HA1 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES 17-340 Source method: isolated from a natural source Details: THE NATIONAL INSTITUTE FOR BIOLOGICAL STANDARDS AND CONTROL (NIBSC) Source: (natural) ![]() ![]() #2: Protein | Mass: 19097.990 Da / Num. of mol.: 3 Fragment: HA2 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES 347-512 Source method: isolated from a natural source Details: THE NATIONAL INSTITUTE FOR BIOLOGICAL STANDARDS AND CONTROL (NIBSC) Source: (natural) ![]() ![]() |
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-Sugars , 2 types, 12 molecules ![](data/chem/img/NAG.gif)
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Sugar | ChemComp-NAG / |
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-Non-polymers , 2 types, 199 molecules ![](data/chem/img/EPE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.04 Å3/Da / Density % sol: 70 % |
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Crystal grow | Details: 0.1 M HEPES PH 7.0, 0.05 M MGCL2, 28-30 % PEG 550 MME |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 23, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9173 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→43.06 Å / Num. obs: 52536 / % possible obs: 73.2 % / Observed criterion σ(I): 3 / Redundancy: 3.3 % / Biso Wilson estimate: 61.3 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2IBX Resolution: 2.71→43.06 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.891 / SU B: 25.011 / SU ML: 0.252 / Cross valid method: THROUGHOUT / ESU R: 1.978 / ESU R Free: 0.356 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. COMPLETENESS VS. RESOLUTION TABLE 999.99 5.83 7336 7045 5.83 4.63 7182 7087 4.63 4.04 7172 6713 4.04 3.67 7228 ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. COMPLETENESS VS. RESOLUTION TABLE 999.99 5.83 7336 7045 5.83 4.63 7182 7087 4.63 4.04 7172 6713 4.04 3.67 7228 7001 3.67 3.41 7131 6988 3.41 3.21 7134 7022 3.21 3.05 7106 6126 3.05 2.91 7148 2824 2.91 2.80 7156 1296 2.80 2.71 7119 434
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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 mean: 52.598 Å2
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Refinement step | Cycle: LAST / Resolution: 2.71→43.06 Å
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