SMTL ID : 8zdw.1

The cryoEM structure of H5N1 HA split from symmetric filament in conformation A

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

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

NAG-NAG.1: 1 residues within 4Å: Chain A: N.39 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain K: N.39 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 1 residues within 4Å: Chain L: N.39 No protein-ligand interaction detected (PLIP)

6 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.2: 3 residues within 4Å: Chain A: N.181, A.254 Chain L: S.233 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 1 residues within 4Å: Chain A: N.302 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 3 residues within 4Å: Chain A: S.233 Chain K: N.181, A.254 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 1 residues within 4Å: Chain K: N.302 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 3 residues within 4Å: Chain K: S.233 Chain L: N.181, A.254 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 1 residues within 4Å: Chain L: N.302 No protein-ligand interaction detected (PLIP)

3 x NAG- GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-GAL-SIA.10: 12 residues within 4Å: Chain L: Y.107, V.147, S.148, S.149, W.165, I.167, H.195, N.198, E.202, L.206, K.234, Q.238 10 PLIP interactions: 10 interactions with chain L Hydrogen bonds: L:K.234, L:N.198, L:Q.238, L:Q.238, L:Y.107, L:S.148, L:S.149, L:N.198, L:N.198, L:Q.238, L:Q.238 Hydrophobic interactions: L:W.165, L:I.167, L:L.206 NAG-GAL-SIA.11: 12 residues within 4Å: Chain K: Y.107, V.147, S.148, S.149, W.165, I.167, H.195, N.198, E.202, L.206, K.234, Q.238 10 PLIP interactions: 10 interactions with chain K Hydrogen bonds: K:K.234, K:N.198, K:Q.238, K:Q.238, K:Y.107, K:S.148, K:S.149, K:N.198, K:N.198, K:Q.238, K:Q.238 Hydrophobic interactions: K:W.165, K:I.167, K:L.206 NAG-GAL-SIA.12: 12 residues within 4Å: Chain A: Y.107, V.147, S.148, S.149, W.165, I.167, H.195, N.198, E.202, L.206, K.234, Q.238 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:K.234, A:N.198, A:Q.238, A:Q.238, A:Y.107, A:S.148, A:S.149, A:N.198, A:N.198, A:Q.238, A:Q.238 Hydrophobic interactions: A:W.165, A:I.167, A:L.206

12 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose

NAG.13: 1 residues within 4Å: Chain A: N.27 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.27 NAG.14: 1 residues within 4Å: Chain A: N.170 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.170 NAG.15: 3 residues within 4Å: Chain B: E.156, N.163, T.165 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.165 NAG.16: 1 residues within 4Å: Chain C: N.67 No protein-ligand interaction detected (PLIP) NAG.17: 3 residues within 4Å: Chain E: E.156, N.163, T.165 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:T.165 NAG.18: 3 residues within 4Å: Chain F: E.156, N.163, T.165 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:T.165 NAG.19: 1 residues within 4Å: Chain I: N.67 No protein-ligand interaction detected (PLIP) NAG.20: 1 residues within 4Å: Chain J: N.67 No protein-ligand interaction detected (PLIP) NAG.21: 1 residues within 4Å: Chain K: N.27 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:N.27 NAG.22: 1 residues within 4Å: Chain K: N.170 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:N.170 NAG.23: 1 residues within 4Å: Chain L: N.27 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:N.27 NAG.24: 1 residues within 4Å: Chain L: N.170 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:N.170

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, R. et al., Multivalent interactions between fully glycosylated influenza virus hemagglutinins mediated by glycans at distinct N-glycosylation sites. To Be Published

Release Date

2024-09-25

Peptides

Hemagglutinin: AKL
Hemagglutinin: BEF
H5M9 Fab, light chain: CIJ
Anti-H5N1 hemagglutinin monoclonal anitbody H5M9 heavy chain: DGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

K
C

L
H

B
B

E
D

F
I

C
R

I
E

J
J

D
U

G
F

H
L

Hemagglutinin

Hemagglutinin

H5M9 Fab, light chain

Anti-H5N1 hemagglutinin monoclonal anitbody H5M9 heavy chain

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