SMTL ID : 8uwa.1

VH1-18 QxxV class antibody 09-1B12 bound to A/Perth/16/2009 H3N2 hemagglutinin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 4.02 Å

Oligo State

hetero-3-3-3-mer

Ligands

2 x NAG- NAG- BMA- MAN: 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.1: 2 residues within 4Å: Chain D: Q.132, N.133 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.9: 2 residues within 4Å: Chain E: N.285, V.297 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.24

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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.2: 3 residues within 4Å: Chain D: N.126, T.128 Ligands: NAG-NAG-BMA-MAN-MAN.5 No protein-ligand interaction detected (PLIP)

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.3: 7 residues within 4Å: Chain D: N.38, A.39 Chain H: A.104, V.105, L.107, D.108, H.111 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.17: 3 residues within 4Å: Chain F: N.285, V.297, N.298 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.18: 4 residues within 4Å: Chain F: G.479, S.480, N.483, T.485 No protein-ligand interaction detected (PLIP)

6 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.4: 6 residues within 4Å: Chain D: N.165, L.244 Chain F: S.219, R.222, P.227 Ligands: NAG-NAG-BMA-MAN-MAN.5 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:R.222 NAG-NAG-BMA-MAN-MAN.5: 9 residues within 4Å: Chain D: A.163, N.165, N.246 Chain F: G.186, D.188, I.217, S.219 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.2, NAG-NAG-BMA-MAN-MAN.4 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.10: 11 residues within 4Å: Chain A: Q.27 Chain E: N.22, G.23, E.41, V.43, Q.44, S.45, S.46, K.292, T.313, K.315 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain E Hydrogen bonds: A:Q.27, E:K.315, E:K.315 NAG-NAG-BMA-MAN-MAN.11: 7 residues within 4Å: Chain E: N.38, T.40, T.318, L.381 Chain G: V.105, L.107, D.108 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:D.108 NAG-NAG-BMA-MAN-MAN.12: 1 residues within 4Å: Chain E: N.63 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.13: 5 residues within 4Å: Chain D: S.219, R.222, N.225 Chain E: N.165, T.167 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.222, D:R.222

2 x NAG- NAG- BMA- MAN: 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.6: 3 residues within 4Å: Chain D: S.45, N.285, V.297 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.8: 8 residues within 4Å: Chain D: I.217, G.218 Chain E: A.163, L.164, N.165, N.246, S.247, T.248 No protein-ligand interaction detected (PLIP)

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.7: 4 residues within 4Å: Chain D: G.479, R.482, N.483, T.485 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain E: A.476, G.479, S.480, N.483 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 2 residues within 4Å: Chain F: N.22, T.24 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA- MAN- MAN- MAN: 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.15: 13 residues within 4Å: Chain A: Y.50, T.57 Chain F: N.38, A.39, T.40, T.318 Chain I: A.104, V.105, I.106, L.107, D.108, Y.110, H.111 2 PLIP interactions: 2 interactions with chain I Hydrophobic interactions: I:D.108 Hydrogen bonds: I:L.107 NAG-NAG-BMA-MAN-MAN-MAN.16: 7 residues within 4Å: Chain E: S.219, R.222, N.225 Chain F: N.165, I.242, L.244 Ligands: NAG.26 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:R.222 Hydrophobic interactions: F:I.242

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

NAG.20: 3 residues within 4Å: Chain D: N.63, Q.75, Y.94 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:Q.75 Hydrogen bonds: D:Q.75 NAG.21: 1 residues within 4Å: Chain D: N.22 No protein-ligand interaction detected (PLIP) NAG.22: 2 residues within 4Å: Chain E: N.126, T.128 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:T.128 NAG.23: 4 residues within 4Å: Chain E: Q.132, N.133, N.152, R.255 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:Q.132, E:R.255 NAG.24: 6 residues within 4Å: Chain A: Q.27, S.28, T.70 Chain E: K.27, N.312, T.313 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:K.27, E:N.312, E:T.313 NAG.25: 3 residues within 4Å: Chain F: N.63, K.92, Y.94 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:N.63, F:K.92, F:Y.94 NAG.26: 5 residues within 4Å: Chain E: I.217 Chain F: A.163, N.246, T.248 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.16 No protein-ligand interaction detected (PLIP) NAG.27: 2 residues within 4Å: Chain F: N.126, T.128 No protein-ligand interaction detected (PLIP) NAG.28: 2 residues within 4Å: Chain F: Q.132, N.133 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ray, R. et al., Eliciting a single amino acid change by vaccination generates antibody protection against group 1 and group 2 influenza A viruses. Immunity (2024)

Release Date

2024-05-08

Peptides

09-1B12 light chain: ABC
Hemagglutinin: DEF
09-1B12 heavy chain: GHI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
G

D
A

E
B

F
C

G
F

H
H

I
U

09-1B12 light chain

Hemagglutinin

09-1B12 heavy chain