SMTL ID : 6bkm.1 (2 other biounits)

Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza virus hemagglutinin E190D mutant apo form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-trimer

Ligands

2 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 3 residues within 4Å: Chain A: N.32, A.33, T.34 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 6 residues within 4Å: Chain A: N.159, T.161, V.236 Chain B: S.213, P.215, W.216 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:W.216 Hydrophobic interactions: A:V.236

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.3: 5 residues within 4Å: Chain A: S.39, N.279, V.291, N.292, K.293 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.293 NAG-NAG.5: 4 residues within 4Å: Chain B: S.39, N.279, V.291, N.292 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN: 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

NAG-NAG-BMA-MAN.4: 7 residues within 4Å: Chain B: N.159, T.161, R.201, V.236 Chain C: S.213, P.215, W.216 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:T.161, B:V.236 Hydrogen bonds: C:W.216, B:R.201

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.6: 6 residues within 4Å: Chain A: S.213, P.215, W.216 Chain C: N.159, T.161, V.236 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:V.236 Hydrogen bonds: A:W.216

5 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.7: 4 residues within 4Å: Chain A: Q.74, N.75, E.113, F.114 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.113 Water bridges: A:Q.74, A:R.144 NAG.8: 1 residues within 4Å: Chain B: N.32 No protein-ligand interaction detected (PLIP) NAG.9: 3 residues within 4Å: Chain B: Q.74, N.75, F.114 No protein-ligand interaction detected (PLIP) NAG.10: 2 residues within 4Å: Chain C: N.32, T.312 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.312 NAG.11: 4 residues within 4Å: Chain C: S.39, N.279, V.291, N.292 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.279, C:V.291, C:N.292

1 x TAM: TRIS(HYDROXYETHYL)AMINOMETHANE(Non-covalent)

TAM.12: 1 residues within 4Å: Chain C: N.167 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.167, C:N.167, C:N.167

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, N.C. et al., A complex epistatic network limits the mutational reversibility in the influenza hemagglutinin receptor-binding site. Nat Commun (2018)

Release Date

2018-02-28

Peptides

Hemagglutinin: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
E

Hemagglutinin

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