SMTL ID : 6mya.1 (1 other biounit)

Crystal structure of InvbP.18715.a.KN11: Influenza hemagglutinin from strain A/Almaty/32/1998

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-trimer

Ligands

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

NAG-NAG.1: 2 residues within 4Å: Chain B: K.24, N.25 No protein-ligand interaction detected (PLIP)

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

NAG.2: 2 residues within 4Å: Chain A: K.24, N.25 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:K.24 NAG.3: 2 residues within 4Å: Chain A: N.13, T.15 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.15 Hydrogen bonds: A:N.13 NAG.4: 1 residues within 4Å: Chain A: N.271 No protein-ligand interaction detected (PLIP) NAG.5: 1 residues within 4Å: Chain A: N.289 No protein-ligand interaction detected (PLIP) NAG.9: 1 residues within 4Å: Chain B: N.13 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.13 NAG.10: 1 residues within 4Å: Chain B: N.271 No protein-ligand interaction detected (PLIP) NAG.11: 1 residues within 4Å: Chain B: N.289 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.289 NAG.12: 1 residues within 4Å: Chain C: N.13 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.13 NAG.13: 2 residues within 4Å: Chain C: N.278, N.289 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.289 NAG.14: 1 residues within 4Å: Chain C: N.271 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.271 NAG.15: 5 residues within 4Å: Chain C: E.476, E.479, S.480, N.483, T.485 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.476, C:N.483

12 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 4 residues within 4Å: Chain A: D.70, L.73, R.115, R.148 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.115 EDO.7: 4 residues within 4Å: Chain A: S.206, P.238, G.239, D.240 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.206, A:S.206 EDO.8: 2 residues within 4Å: Chain A: L.427 Chain C: L.427 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.424, A:N.424 EDO.16: 5 residues within 4Å: Chain B: N.209 Chain C: D.96, H.183, E.215, N.230 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C Water bridges: B:N.209, B:N.209 Hydrogen bonds: C:D.96, C:E.215, C:N.230 EDO.17: 6 residues within 4Å: Chain C: N.58, A.60, G.90, A.91, F.97, Y.100 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.58, C:A.91 Water bridges: C:F.97 EDO.18: 5 residues within 4Å: Chain C: T.135, A.136, Q.225 Ligands: EDO.19, EDO.20 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:A.136, C:Q.225 Water bridges: C:V.134, C:S.144 EDO.19: 6 residues within 4Å: Chain C: A.136, S.137, R.223, D.224, Q.225 Ligands: EDO.18 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.223 EDO.20: 5 residues within 4Å: Chain C: K.132, V.134, W.152, L.193 Ligands: EDO.18 No protein-ligand interaction detected (PLIP) EDO.21: 5 residues within 4Å: Chain C: A.91, P.94, G.95, V.222, R.223 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.95, C:R.223, C:R.223 Water bridges: C:G.95 EDO.22: 4 residues within 4Å: Chain B: N.207, Y.208 Chain C: G.95, D.96 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain C Water bridges: B:S.206, B:S.206, B:Y.208, C:G.95, C:D.96, C:F.97 Hydrogen bonds: C:D.96, C:D.96 EDO.23: 2 residues within 4Å: Chain C: H.140, S.145 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:H.140, C:S.145, C:S.145 EDO.24: 4 residues within 4Å: Chain C: S.206, P.238, G.239, D.240 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:S.206, C:S.206, C:P.238, C:D.240 Water bridges: C:T.241

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ghafoori, S.M. et al., Structural characterisation of hemagglutinin from seven Influenza A H1N1 strains reveal diversity in the C05 antibody recognition site. Sci Rep (2023)

Release Date

2018-11-14

Peptides

Hemagglutinin: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Hemagglutinin

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