SMTL ID : 9bdg.1

Influenza A virus Hemagglutinin H3/Darwin/6/2021 in complex with Fab ADI-85647

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN-MAN-MAN.1: 16 residues within 4Å: Chain A: E.123, S.124, N.126, W.127, V.130, Q.132, N.133, R.255 Chain F: E.1, V.2, Y.32, W.102, L.114 Chain I: K.45, L.56 Ligands: NAG.15 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.2: 7 residues within 4Å: Chain A: A.163, N.165, R.201, N.246, S.247, T.248 Chain C: I.217 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.248 NAG-NAG-BMA.5: 10 residues within 4Å: Chain A: I.217, G.218 Chain B: A.163, Q.164, N.165, R.201, T.203, N.246, T.248 Ligands: NAG-NAG-BMA-MAN-MAN.7 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.11: 9 residues within 4Å: Chain B: I.217 Chain C: A.163, Q.164, N.165, R.201, T.203, N.246, S.247, T.248 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.3: 7 residues within 4Å: Chain A: N.165, T.167, L.244 Chain C: S.219, P.221, R.222, D.225 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.222, C:R.222 NAG-NAG-BMA-MAN-MAN.7: 12 residues within 4Å: Chain A: T.187, S.219, R.220, P.221, R.222, R.224, D.225 Chain B: N.165, T.167, I.242, L.244 Ligands: NAG-NAG-BMA.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.224, A:R.222 Hydrophobic interactions: A:R.222 NAG-NAG-BMA-MAN-MAN.10: 8 residues within 4Å: Chain B: T.187, R.220, P.221, R.222, D.225 Chain C: N.165, T.167, I.242 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:R.222

5 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.4: 5 residues within 4Å: Chain A: N.45, N.285, V.297, N.298, E.398 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain B: N.285, V.297, N.298, E.398 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain B: N.38, N.378, L.381 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.381 NAG-NAG.13: 5 residues within 4Å: Chain C: N.45, N.285, V.297, N.298, E.398 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain C: N.38, T.318, N.378, L.381 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.378

2 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN-MAN-MAN.6: 16 residues within 4Å: Chain B: E.123, S.124, N.126, W.127, T.128, G.129, V.130, Q.132, N.133, R.255 Chain D: V.2, Y.32, W.102 Chain G: L.56, G.57 Ligands: NAG.18 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.129, B:V.130 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.12: 11 residues within 4Å: Chain C: S.124, N.126, W.127, V.130, Q.132, N.133, R.255 Chain E: V.2, Y.32, L.114 Chain H: L.56 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.126, C:G.129, C:Q.132

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

NAG.15: 2 residues within 4Å: Chain A: N.126 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.126 NAG.16: 1 residues within 4Å: Chain A: N.63 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.63, A:N.63 NAG.17: 3 residues within 4Å: Chain A: N.38, T.40, T.318 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.38, A:N.38, A:T.318 NAG.18: 2 residues within 4Å: Chain B: N.126 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.6 No protein-ligand interaction detected (PLIP) NAG.19: 1 residues within 4Å: Chain B: N.63 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.63 NAG.20: 1 residues within 4Å: Chain C: N.126 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.126, C:T.128 NAG.21: 2 residues within 4Å: Chain C: N.63, R.92 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.63, C:R.92

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maurer, D. et al., Influenza A virus Hemagglutinin H3/Darwin/6/2021 in complex with Fab ADI-85647. To Be Published

Release Date

2024-11-13

Peptides

Hemagglutinin: ABC
Fab ADI-85647 Heavy chain: DEF
Ig-like domain-containing protein: GHI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

Hemagglutinin

Fab ADI-85647 Heavy chain

Ig-like domain-containing protein

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