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- PDB-5ajm: H5 (VN1194) Asn186Lys Mutant Haemagglutinin in Complex with Avian... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ajm | ||||||||||||
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Title | H5 (VN1194) Asn186Lys Mutant Haemagglutinin in Complex with Avian Receptor Analogue 3'SLN | ||||||||||||
![]() | (HAEMAGGLUTININ ...) x 2 | ||||||||||||
![]() | VIRAL PROTEIN / HAEMAGGLUTININ / HAEMAGGLUTININ MUTANT / H5N1 / INFLUENZA / SIALIC ACID / GLYCOPROTEIN / VIRUS RECEPTOR / AVIAN FLU / SIALYLLACTOSAMINE / 3SLN / 3'SLN / 6SLN / 6'SLN / LSTA | ||||||||||||
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 | ![]() ![]() ![]() | ||||||||||||
![]() | Xiong, X. / Xiao, H. / Martin, S.R. / Coombs, P.J. / Liu, J. / Collins, P.J. / Vachieri, S.G. / Walker, P.A. / Lin, Y.P. / McCauley, J.W. ...Xiong, X. / Xiao, H. / Martin, S.R. / Coombs, P.J. / Liu, J. / Collins, P.J. / Vachieri, S.G. / Walker, P.A. / Lin, Y.P. / McCauley, J.W. / Gamblin, S.J. / Skehel, J.J. | ||||||||||||
![]() | ![]() Title: Enhanced Human Receptor Binding by H5 Haemagglutinins. Authors: Xiong, X. / Xiao, H. / Martin, S.R. / Coombs, P.J. / Liu, J. / Collins, P.J. / Vachieri, S.G. / Walker, P.A. / Lin, Y.P. / Mccauley, J.W. / Gamblin, S.J. / 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 | ![]() | 219.5 KB | Display | ![]() |
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PDB format | ![]() | 178.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 21.8 KB | Display | |
Data in CIF | ![]() | 30.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4cqpC ![]() 4cqqC ![]() 4cqrC ![]() 4cqsC ![]() 4cquC ![]() 4cqvC ![]() 4cqwC ![]() 4cqxC ![]() 4cqyC ![]() 4cqzC ![]() 4cr0C ![]() 4bgwS 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
-HAEMAGGLUTININ ... , 2 types, 2 molecules AB
#1: Protein | Mass: 36965.844 Da / Num. of mol.: 1 Fragment: HA1 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES 17-342 Source method: isolated from a natural source Source: (natural) ![]() Variant: ASN186LYS MUTANT / References: UniProt: Q6DQ34 |
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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 natural source Source: (natural) ![]() Variant: ASN186LYS MUTANT / References: UniProt: Q6DQ34 |
-Sugars , 5 types, 6 molecules ![](data/chem/img/NAG.gif)
#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#4: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#5: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / 3'-sialyl-N-acetyllactosamine |
#6: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#7: Sugar |
-Non-polymers , 2 types, 164 molecules ![](data/chem/img/MPO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#8: Chemical | ChemComp-MPO / |
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#9: Water | ChemComp-HOH / |
-Details
Sequence details | MULTIBASIC |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.74 Å3/Da / Density % sol: 67 % / Description: NONE |
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Crystal grow | Details: 0.1 M HEPES/MOPS PH 7.0, 0.05 M MGCL2, 28-30% PEG 550 MME, SEEDED WITH CRUSHED WILD-TYPE VN1194 HA CRYSTALS. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→50.79 Å / Num. obs: 33498 / % possible obs: 99.2 % / Observed criterion σ(I): 2.7 / Redundancy: 7.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2.45→2.58 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.7 / % possible all: 98.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4BGW Resolution: 2.45→150.99 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.947 / SU B: 16.592 / SU ML: 0.184 / Cross valid method: THROUGHOUT / ESU R: 0.268 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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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: 78.353 Å2
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Refinement step | Cycle: LAST / Resolution: 2.45→150.99 Å
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Refine LS restraints |
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