SMTL ID : 9mq2.1

Cryo-EM map of H5 HA (A/Jiangsu/NJ210/2023) in complex with monoclonal fab 12G1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.06 Å

Oligo State

hetero-3-1-1-3-mer

Ligands

3 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.1: 3 residues within 4Å: Chain A: N.181, A.254 Chain B: S.233 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.2: 6 residues within 4Å: Chain B: N.181, D.252, A.254 Chain D: P.104, Y.107 Chain E: Y.33 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:P.104 Hydrogen bonds: D:Y.107 NAG-NAG-FUC.3: 6 residues within 4Å: Chain A: S.233, Q.234 Chain C: N.181, D.252, D.253, A.254 No protein-ligand interaction detected (PLIP)

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

NAG.4: 4 residues within 4Å: Chain A: A.25, N.26, N.27 Chain F: Q.15 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:Q.15 NAG.5: 1 residues within 4Å: Chain A: N.39 No protein-ligand interaction detected (PLIP) NAG.6: 2 residues within 4Å: Chain A: N.291, N.302 No protein-ligand interaction detected (PLIP) NAG.7: 1 residues within 4Å: Chain B: N.302 No protein-ligand interaction detected (PLIP) NAG.8: 1 residues within 4Å: Chain B: N.27 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.27 NAG.9: 2 residues within 4Å: Chain B: Q.31, N.39 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.39 NAG.10: 2 residues within 4Å: Chain C: N.291, N.302 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.302 NAG.11: 2 residues within 4Å: Chain C: N.27 Chain H: Q.15 No protein-ligand interaction detected (PLIP) NAG.12: 3 residues within 4Å: Chain C: Q.31, K.38, N.39 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:K.38 Hydrogen bonds: C:Q.31 NAG.13: 3 residues within 4Å: Chain F: E.150, N.154, T.156 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:E.150 NAG.14: 1 residues within 4Å: Chain H: N.154 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pena Alzua, G. et al., Human Monoclonal Antibodies that Target Clade 2.3.4.4b H5N1 Hemagglutinin. To Be Published

Release Date

2025-11-05

Peptides

Hemagglutinin HA1: ABC
12G1 Heavy Chain Fab: D
12G1 Light Chain Fab: E
Hemagglutinin HA2: FGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

E
L

F
a

G
b

H
c

Hemagglutinin HA1

12G1 Heavy Chain Fab

12G1 Light Chain Fab

Hemagglutinin HA2

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