SMTL ID : 8tx3.1

Fab 3864-6 in complex with influenza HA H3-VIC11

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

9 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.1: 2 residues within 4Å: Chain A: T.53, N.54 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.2: 9 residues within 4Å: Chain A: N.181, T.183, I.258, L.260 Chain C: Y.235, P.237, R.238, N.241 Ligands: NAG-NAG-BMA-MAN-MAN.3 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:R.238 Hydrophobic interactions: A:I.258 NAG-NAG-BMA-MAN-MAN.3: 9 residues within 4Å: Chain A: A.179, N.181, R.217, N.262, S.263, T.264 Chain C: T.203, I.233 Ligands: NAG-NAG-BMA-MAN-MAN.2 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.5: 2 residues within 4Å: Chain C: N.38, G.39 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.6: 10 residues within 4Å: Chain C: N.181, T.183, I.258, L.260 Chain E: Y.235, P.237, R.238, N.241 Ligands: NAG-NAG-BMA-MAN-MAN.7, NAG-NAG-BMA-MAN-MAN.7 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain E Hydrophobic interactions: C:I.258 Hydrogen bonds: E:R.238 NAG-NAG-BMA-MAN-MAN.7: 10 residues within 4Å: Chain C: A.179, N.181, R.217, T.219, N.262, S.263, T.264 Chain E: I.233, Y.235 Ligands: NAG-NAG-BMA-MAN-MAN.6 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.9: 2 residues within 4Å: Chain E: N.54, A.55 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.10: 10 residues within 4Å: Chain A: Y.235, P.237, R.238, N.241 Chain E: N.181, T.183, I.258, L.260 Ligands: NAG-NAG-BMA-MAN-MAN.11, NAG-NAG-BMA-MAN-MAN.11 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:R.238, A:R.238 Hydrophobic interactions: E:I.258 NAG-NAG-BMA-MAN-MAN.11: 9 residues within 4Å: Chain A: I.233 Chain E: A.179, L.180, N.181, R.217, N.262, S.263, T.264 Ligands: NAG-NAG-BMA-MAN-MAN.10 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:T.264, E:T.264

3 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.4: 4 residues within 4Å: Chain A: N.61, N.301, V.313 Chain B: E.69 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 4 residues within 4Å: Chain C: N.61, N.301, V.313 Chain D: E.69 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 5 residues within 4Å: Chain E: N.61, N.301, V.313, N.314 Chain F: E.69 No protein-ligand interaction detected (PLIP)

14 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Post Translational Modification)

NAG.13: 1 residues within 4Å: Chain A: N.38 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.38 NAG.14: 3 residues within 4Å: Chain A: E.78, N.79, Y.110 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.110 NAG.15: 2 residues within 4Å: Chain A: N.142, T.144 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.144 NAG.16: 2 residues within 4Å: Chain A: N.149, R.271 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.149, A:R.271 NAG.17: 2 residues within 4Å: Chain B: N.154, T.156 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.154 NAG.18: 1 residues within 4Å: Chain C: N.38 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.38 NAG.19: 3 residues within 4Å: Chain C: E.78, N.79, Y.110 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.110 Hydrogen bonds: C:Y.110 NAG.20: 2 residues within 4Å: Chain C: N.142, T.144 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.144 NAG.21: 2 residues within 4Å: Chain C: N.149, R.271 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.149, C:R.271 NAG.22: 1 residues within 4Å: Chain D: N.154 No protein-ligand interaction detected (PLIP) NAG.23: 1 residues within 4Å: Chain E: N.38 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.38 NAG.24: 3 residues within 4Å: Chain E: E.78, N.79, Y.110 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Y.110 NAG.25: 2 residues within 4Å: Chain E: N.142, T.144 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:T.144 NAG.26: 2 residues within 4Å: Chain E: N.149, R.271 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.149, E:R.271

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rawi, R. et al., The N terminus of H3-influenza hemagglutinin as a site-of-vulnerability to neutralizing antibody. Structure (2025)

Release Date

2024-09-11

Peptides

Hemagglutinin: ACE
Hemagglutinin: BDF
Fab 3864-6 Heavy Chain: GIK
Fab 3864-6 Light Chain: HJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
G

B
B

D
D

F
I

G
H

I
E

K
F

H
L

J
J

L
K

Hemagglutinin

Hemagglutinin

Fab 3864-6 Heavy Chain

Fab 3864-6 Light Chain

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