SMTL ID : 6q20.1

Crystal structure of human 1E01 Fab in complex with influenza virus neuraminidase from A/Japan/305/1957 (H2N2)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

hetero-4-4-4-mer

Ligands

4 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-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-MAN-MAN.1: 11 residues within 4Å: Chain A: N.124 Chain B: L.54 Chain J: D.254, S.255, Q.315, V.316, N.317, R.318, Y.377, G.378, T.379 4 PLIP interactions: 4 interactions with chain J Hydrogen bonds: J:N.317, J:R.318, J:N.317, J:N.317, J:R.318 Water bridges: J:Y.377 NAG-NAG-BMA-MAN-MAN-MAN-MAN.6: 11 residues within 4Å: Chain D: N.124 Chain E: L.54 Chain G: D.254, S.255, Q.315, V.316, N.317, R.318, Y.377, G.378, T.379 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:N.317, G:R.318, G:N.317, G:N.317, G:R.318 Water bridges: G:Y.377 NAG-NAG-BMA-MAN-MAN-MAN-MAN.11: 11 residues within 4Å: Chain A: D.254, S.255, Q.315, V.316, N.317, R.318, Y.377, G.378, T.379 Chain G: N.124 Chain H: L.54 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.317, A:R.318, A:N.317, A:N.317, A:R.318 Water bridges: A:Y.377 NAG-NAG-BMA-MAN-MAN-MAN-MAN.16: 11 residues within 4Å: Chain D: D.254, S.255, Q.315, V.316, N.317, R.318, Y.377, G.378, T.379 Chain J: N.124 Chain K: L.54 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.317, D:R.318, D:N.317, D:N.317, D:R.318 Water bridges: D:Y.377

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

NAG-NAG.2: 3 residues within 4Å: Chain A: N.70, W.361, I.393 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain D: N.70, W.361, I.393 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain G: N.70, W.361, I.393 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain J: N.70, W.361, I.393 No protein-ligand interaction detected (PLIP)

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

NAG.3: 3 residues within 4Å: Chain A: N.10, N.158, Y.208 No protein-ligand interaction detected (PLIP) NAG.8: 3 residues within 4Å: Chain D: N.10, N.158, Y.208 No protein-ligand interaction detected (PLIP) NAG.13: 3 residues within 4Å: Chain G: N.10, N.158, Y.208 No protein-ligand interaction detected (PLIP) NAG.18: 3 residues within 4Å: Chain J: N.10, N.158, Y.208 No protein-ligand interaction detected (PLIP)

8 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.4: 10 residues within 4Å: Chain A: D.217, G.221, S.222, D.248, P.250, R.268, G.269, N.270, P.271, G.272 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:P.271 CA.5: 3 residues within 4Å: Ligands: CA.10, CA.15, CA.20 No protein-ligand interaction detected (PLIP) CA.9: 10 residues within 4Å: Chain D: D.217, G.221, S.222, D.248, P.250, R.268, G.269, N.270, P.271, G.272 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:P.271 CA.10: 3 residues within 4Å: Ligands: CA.5, CA.15, CA.20 No protein-ligand interaction detected (PLIP) CA.14: 10 residues within 4Å: Chain G: D.217, G.221, S.222, D.248, P.250, R.268, G.269, N.270, P.271, G.272 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:P.271 CA.15: 3 residues within 4Å: Ligands: CA.5, CA.10, CA.20 No protein-ligand interaction detected (PLIP) CA.19: 10 residues within 4Å: Chain J: D.217, G.221, S.222, D.248, P.250, R.268, G.269, N.270, P.271, G.272 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:P.271 CA.20: 3 residues within 4Å: Ligands: CA.5, CA.10, CA.15 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stadlbauer, D. et al., Broadly protective human antibodies that target the active site of influenza virus neuraminidase. Science (2019)

Release Date

2019-10-23

Peptides

Neuraminidase: ADGJ
1E01 Fab kappa light chain: BEHK
1E01 Fab IgG1 heavy chain: CFIL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
A

G
A

J
A

B
L

E
L

H
L

K
L

C
H

F
H

I
H

L
H

Neuraminidase

1E01 Fab kappa light chain

1E01 Fab IgG1 heavy chain