SMTL ID : 6pdx.1

Crystal structure of C585 Fab in complex with influenza virus hemagglutinin from A/Switzerland/9715293/2013 (H3N2)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.99 Å

Oligo State

hetero-3-3-3-mer

Ligands

13 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.1: 3 residues within 4Å: Chain A: Q.132, N.133 Chain B: W.74 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 6 residues within 4Å: Chain A: N.165, T.167 Chain G: S.219, P.221, R.222 Ligands: NAG-NAG-BMA.6 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:R.222, G:R.222 NAG-NAG-BMA.4: 4 residues within 4Å: Chain A: N.38, T.40, T.318, L.381 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 3 residues within 4Å: Chain A: E.62, N.63, Y.94 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 9 residues within 4Å: Chain A: A.163, L.164, N.165, N.246, T.248 Chain G: T.187, D.188, S.219 Ligands: NAG-NAG-BMA.2 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 1 residues within 4Å: Chain A: N.483 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 8 residues within 4Å: Chain A: D.188, I.217, G.218 Chain D: A.163, L.164, N.165, N.246 Ligands: NAG-NAG-BMA.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.188 NAG-NAG-BMA.9: 6 residues within 4Å: Chain A: S.219, R.222 Chain D: N.165, T.167, I.242 Ligands: NAG-NAG-BMA.8 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:I.242 Hydrogen bonds: A:R.222 NAG-NAG-BMA.12: 3 residues within 4Å: Chain D: Q.132, N.133 Chain E: W.74 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:W.74 NAG-NAG-BMA.14: 2 residues within 4Å: Chain G: N.133 Chain H: W.74 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 4 residues within 4Å: Chain D: S.219, R.222 Chain G: N.165 Ligands: NAG-NAG-BMA.16 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.222 NAG-NAG-BMA.16: 8 residues within 4Å: Chain D: D.188, I.217, G.218 Chain G: A.163, N.246, S.247, T.248 Ligands: NAG-NAG-BMA.15 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.17: 2 residues within 4Å: Chain G: N.285, V.297 No protein-ligand interaction detected (PLIP)

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.3: 3 residues within 4Å: Chain A: N.285, V.297, N.298 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain D: N.285, V.297, N.298 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 5 residues within 4Å: Chain D: N.38, A.39, T.318, N.378, L.381 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain D: E.62, N.63, Y.94 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 3 residues within 4Å: Chain G: N.38, A.39, N.378 No protein-ligand interaction detected (PLIP)

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

NAG.19: 2 residues within 4Å: Chain D: N.483, T.485 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:N.483 Hydrogen bonds: D:T.485

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Qiu, Y. et al., Mapping of a Novel H3-Specific Broadly Neutralizing Monoclonal Antibody Targeting the Hemagglutinin Globular Head Isolated from an Elite Influenza Virus-Immunized Donor Exhibiting Serological Breadth. J.Virol. (2020)

Release Date

2019-12-18

Peptides

Hemagglutinin: ADG
C585 Fab heavy chain: BEH
C585 Fab light chain: CFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
B

G
C

B
H

E
M

H
O

C
L

F
N

I
P

Hemagglutinin

C585 Fab heavy chain

C585 Fab light chain