SMTL ID : 6u02.1

CryoEM-derived model of NA-63 Fab in complex with N9 Shanghai2

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-4-mer

Ligands

4 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-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-MAN.1: 18 residues within 4Å: Chain A: N.160, N.161 Chain J: R.288, N.290, D.291, R.324, I.326, T.328, E.335, K.349, P.350, I.351, Q.352, G.353, F.413, L.414, G.415, Q.416 2 PLIP interactions: 2 interactions with chain J Hydrophobic interactions: J:F.413 Hydrogen bonds: J:G.353 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.2: 18 residues within 4Å: Chain A: R.288, N.290, D.291, R.324, I.326, T.328, E.335, K.349, P.350, I.351, Q.352, G.353, F.413, L.414, G.415, Q.416 Chain D: N.160, N.161 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.413 Hydrogen bonds: A:G.353 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.3: 18 residues within 4Å: Chain D: R.288, N.290, D.291, R.324, I.326, T.328, E.335, K.349, P.350, I.351, Q.352, G.353, F.413, L.414, G.415, Q.416 Chain G: N.160, N.161 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:F.413 Hydrogen bonds: D:G.353 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.4: 18 residues within 4Å: Chain G: R.288, N.290, D.291, R.324, I.326, T.328, E.335, K.349, P.350, I.351, Q.352, G.353, F.413, L.414, G.415, Q.416 Chain J: N.160, N.161 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:F.413 Hydrogen bonds: G:G.353

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

NAG.5: 4 residues within 4Å: Chain A: N.43, F.44, N.46, N.195 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.195 NAG.6: 2 residues within 4Å: Chain A: N.106, W.398 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.106, A:W.398 NAG.7: 4 residues within 4Å: Chain D: N.43, F.44, N.46, N.195 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.195 NAG.8: 2 residues within 4Å: Chain D: N.106, W.398 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.106, D:W.398 NAG.9: 4 residues within 4Å: Chain G: N.43, F.44, N.46, N.195 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:N.195 NAG.10: 2 residues within 4Å: Chain G: N.106, W.398 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:N.106, G:W.398 NAG.11: 4 residues within 4Å: Chain J: N.43, F.44, N.46, N.195 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:N.195 NAG.12: 2 residues within 4Å: Chain J: N.106, W.398 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:N.106, J:W.398

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhu, X. et al., Structural Basis of Protection against H7N9 Influenza Virus by Human Anti-N9 Neuraminidase Antibodies. Cell Host Microbe (2019)

Release Date

2019-12-04

Peptides

Neuraminidase: ADGJ
Fab-63 Light Chain: BEHK
Fab-63 Heavy Chain: CFIL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
B

G
E

J
J

B
L

E
C

H
F

K
I

C
H

F
D

I
G

L
K

Neuraminidase

Fab-63 Light Chain

Fab-63 Heavy Chain

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