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

Crystal structure of Influenza hemagglutinin from strain A/Melbourne/1/1946(H1N1)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

homo-trimer

Ligands

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.1: 2 residues within 4Å: Chain B: P.85, N.271 No protein-ligand interaction detected (PLIP)

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

NAG.2: 1 residues within 4Å: Chain A: N.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.13 NAG.3: 3 residues within 4Å: Chain A: T.15, N.25, T.27 No protein-ligand interaction detected (PLIP) NAG.4: 1 residues within 4Å: Chain A: N.271 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.271 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: 2 residues within 4Å: Chain B: N.25, T.27 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.27 NAG.11: 2 residues within 4Å: Chain B: N.278, 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 No protein-ligand interaction detected (PLIP) NAG.13: 1 residues within 4Å: Chain C: N.25 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.25 NAG.14: 1 residues within 4Å: Chain C: N.289 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.289

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

EDO.6: 7 residues within 4Å: Chain A: W.125, P.126, K.127, H.128, K.162, L.163, S.164 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.127, A:H.128, A:S.164, A:S.164 EDO.7: 5 residues within 4Å: Chain A: N.58, A.60, G.90, I.91, Y.100 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.58, A:I.91 Water bridges: A:F.97 EDO.15: 4 residues within 4Å: Chain C: S.124, K.162, L.163, S.164 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.124, C:S.164 EDO.16: 4 residues within 4Å: Chain C: P.299, A.394, G.396, D.414 2 PLIP interactions: 2 interactions with chain C Water bridges: C:K.397, C:D.414

1 x K: POTASSIUM ION(Non-covalent)

K.8: 2 residues within 4Å: Chain A: D.96, F.97 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.96, A:F.97, H2O.1, H2O.2, H2O.3

1 x NA: SODIUM ION(Non-functional Binders)

NA.17: 2 residues within 4Å: Chain C: D.96, F.97 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:F.97 Water bridges: C:D.99

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

2019-05-15

Peptides

Hemagglutinin: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Hemagglutinin

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