SMTL ID : 6ona.1

Crystal structure of Influenza hemagglutinin from strain A/Hickox/JY2/1940

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 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: 6 residues within 4Å: Chain A: N.66, E.68, N.89, C.92, S.139, R.223 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 7 residues within 4Å: Chain B: N.66, E.68, E.88, N.89, C.92, S.139, R.223 No protein-ligand interaction detected (PLIP)

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: 1 residues within 4Å: Chain C: N.25 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 7 residues within 4Å: Chain C: N.66, E.68, E.88, N.89, C.92, S.139, R.223 No protein-ligand interaction detected (PLIP)

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

NAG.5: 1 residues within 4Å: Chain A: N.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.13 NAG.6: 1 residues within 4Å: Chain A: N.25 No protein-ligand interaction detected (PLIP) NAG.7: 2 residues within 4Å: Chain A: N.164, E.245 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.164, A:E.245 NAG.13: 1 residues within 4Å: Chain B: N.13 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.13 NAG.14: 2 residues within 4Å: Chain B: N.164, E.245 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.164 NAG.15: 1 residues within 4Å: Chain B: N.271 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.271 NAG.16: 2 residues within 4Å: Chain B: N.483, T.485 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.483 NAG.21: 4 residues within 4Å: Chain C: S.38, H.39, N.40, N.289 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.289 Water bridges: C:E.36 NAG.22: 2 residues within 4Å: Chain C: N.483, T.485 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.485 NAG.23: 4 residues within 4Å: Chain C: P.85, T.269, S.270, N.271 No protein-ligand interaction detected (PLIP) NAG.29: 1 residues within 4Å: Chain C: N.13 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.13

7 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.8: 5 residues within 4Å: Chain A: W.343, H.354, Y.363, N.464, C.466 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.363, A:N.464 PEG.9: 3 residues within 4Å: Chain A: T.318, I.377, T.378 No protein-ligand interaction detected (PLIP) PEG.17: 4 residues within 4Å: Chain B: W.343, H.354, Y.363, C.466 No protein-ligand interaction detected (PLIP) PEG.18: 4 residues within 4Å: Chain B: T.318, W.350, T.378, V.381 No protein-ligand interaction detected (PLIP) PEG.24: 4 residues within 4Å: Chain C: W.343, H.354, Y.363, N.464 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.363, C:Y.363, C:N.464 PEG.25: 4 residues within 4Å: Chain C: S.369, N.372, F.439, N.443 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.372 PEG.26: 3 residues within 4Å: Chain C: V.32, T.318, W.350 No protein-ligand interaction detected (PLIP)

7 x CL: CHLORIDE ION(Non-functional Binders)

CL.10: 3 residues within 4Å: Chain A: K.380, R.435 Chain B: V.21 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain A: H.10, T.29, H.30, W.350 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain A: L.431, R.435 Chain B: L.431, R.435 Chain C: R.435 Ligand excluded by PLIP CL.19: 3 residues within 4Å: Chain B: K.380, R.435 Chain C: V.21 Ligand excluded by PLIP CL.20: 4 residues within 4Å: Chain B: H.10, T.29, H.30, W.350 Ligand excluded by PLIP CL.27: 4 residues within 4Å: Chain A: V.21, L.22 Chain C: K.380, R.435 Ligand excluded by PLIP CL.28: 3 residues within 4Å: Chain C: T.29, H.30, W.350 Ligand excluded by PLIP

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

2019-05-01

Peptides

Hemagglutinin: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Hemagglutinin