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

Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza virus hemagglutinin E190D mutant in complex with 6'-SLN

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 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: 5 residues within 4Å: Chain A: N.159, V.236 Chain B: S.213, P.215, W.216 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.236 Hydrogen bonds: B:W.216

3 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: 4 residues within 4Å: Chain A: S.39, N.279, V.291, N.292 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain B: S.39, N.279, V.291, N.292 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain C: S.39, N.279, V.291, N.292 No protein-ligand interaction detected (PLIP)

2 x NAG- GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-GAL-SIA.4: 11 residues within 4Å: Chain A: Y.92, G.129, S.130, N.131, W.147, H.177, D.184, L.188, G.219, L.220, S.222 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.219, A:G.129, A:N.131, A:N.131, A:H.177, A:D.184, A:S.222 NAG-GAL-SIA.7: 11 residues within 4Å: Chain B: Y.92, G.129, S.130, N.131, W.147, H.177, D.184, L.188, G.219, L.220, S.222 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.219, B:Y.92, B:G.129, B:N.131, B:N.131, B:H.177, B:S.222 Water bridges: B:G.129, B:G.129

2 x NAG- NAG- BMA- MAN- MAN: 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

NAG-NAG-BMA-MAN-MAN.5: 6 residues within 4Å: Chain B: N.159, T.161, 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 NAG-NAG-BMA-MAN-MAN.8: 6 residues within 4Å: Chain A: S.213, P.215, W.216 Chain C: N.159, T.161, R.201 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:W.216, C:R.201, A:W.216

1 x GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose(Non-covalent)

GAL-SIA.10: 12 residues within 4Å: Chain C: Y.92, G.128, G.129, S.130, N.131, W.147, H.177, D.184, L.188, G.219, L.220, S.222 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:G.219, C:Y.92, C:G.129, C:N.131, C:N.131, C:H.177, C:S.222 Water bridges: C:G.129, C:G.129

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

NAG.11: 3 residues within 4Å: Chain A: Q.74, N.75, F.114 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.75 Water bridges: A:N.75, A:R.144 NAG.12: 1 residues within 4Å: Chain B: N.32 No protein-ligand interaction detected (PLIP) NAG.13: 3 residues within 4Å: Chain B: Q.74, N.75, F.114 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.75 NAG.15: 2 residues within 4Å: Chain C: N.32, T.312 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.312 Water bridges: C:N.32

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

TAM.14: 4 residues within 4Å: Chain B: T.125, Q.126, N.127, G.128 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.127 Water bridges: B:G.128, B:G.129 TAM.16: 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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