SMTL ID : 7k37.1

Structure of full-length influenza HA with a head-binding antibody at pH 7.8

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(Post Translational Modification)

NAG-NAG.1: 1 residues within 4Å: Chain A: N.54 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain C: N.54 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 1 residues within 4Å: Chain E: N.54 No protein-ligand interaction detected (PLIP)

3 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.2: 7 residues within 4Å: Chain A: N.181, T.183, V.258 Chain C: S.235, R.236, P.237, W.238 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:W.238 Hydrophobic interactions: A:V.258 NAG-NAG-BMA-MAN-MAN.5: 7 residues within 4Å: Chain C: N.181, T.183, V.258 Chain E: S.235, R.236, P.237, W.238 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain C Hydrogen bonds: E:W.238 Hydrophobic interactions: C:V.258 NAG-NAG-BMA-MAN-MAN.8: 7 residues within 4Å: Chain A: S.235, R.236, P.237, W.238 Chain E: N.181, T.183, V.258 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:W.238 Hydrophobic interactions: E:V.258

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[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-MAN-MAN-MAN-MAN.3: 12 residues within 4Å: Chain A: S.61, N.301, V.313, K.315 Chain H: Y.54, D.55, G.56, Q.57, T.58, T.72, T.74, G.104 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:T.58, H:T.58 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.6: 12 residues within 4Å: Chain A: N.189 Chain C: S.61, N.301, V.313, K.315 Chain J: Y.54, D.55, G.56, Q.57, T.58, T.74, G.104 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:T.58, J:T.58 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.9: 11 residues within 4Å: Chain E: S.61, N.301, V.313, K.315 Chain L: Y.54, D.55, G.56, Q.57, T.58, T.74, G.104 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:T.58, L:T.58

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

NAG.10: 1 residues within 4Å: Chain A: N.38 No protein-ligand interaction detected (PLIP) NAG.11: 5 residues within 4Å: Chain A: Q.96, N.97, E.135, F.136, I.137 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.97, A:E.135 NAG.12: 3 residues within 4Å: Chain B: E.150, N.154, T.156 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.150, B:N.154 NAG.13: 1 residues within 4Å: Chain C: N.38 No protein-ligand interaction detected (PLIP) NAG.14: 5 residues within 4Å: Chain C: Q.96, N.97, E.135, F.136, I.137 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.97, C:E.135 NAG.15: 3 residues within 4Å: Chain D: E.150, N.154, T.156 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.150, D:N.154 NAG.16: 1 residues within 4Å: Chain E: N.38 No protein-ligand interaction detected (PLIP) NAG.17: 5 residues within 4Å: Chain E: Q.96, N.97, E.135, F.136, I.137 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.97, E:E.135 NAG.18: 3 residues within 4Å: Chain F: E.150, N.154, T.156 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:E.150, F:N.154

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gao, J. et al., Structural intermediates in the low pH-induced transition of influenza hemagglutinin. Plos Pathog. (2020)

Release Date

2020-11-11

Peptides

Hemagglutinin: ACE
Hemagglutinin: BDF
antibody Fab light chain: GIK
antibody Fab heavy chain: HJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

G
G

I
I

K
K

H
H

J
J

L
L

Hemagglutinin

Hemagglutinin

antibody Fab light chain

antibody Fab heavy chain

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