SMTL ID : 6lxj.1

Crystal structure of human Z2B3 Fab in complex with influenza virus neuraminidase from A/Anhui/1/2013 (H7N9)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

hetero-4-4-4-mer

Ligands

1 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.1: 8 residues within 4Å: Chain A: N.65, W.357 Chain E: K.19, A.72, D.73, E.74, S.75, Y.80 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:K.19, E:E.74, E:S.75

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.2: 18 residues within 4Å: Chain A: N.119, N.120 Chain B: R.247, N.249, D.250, R.283, I.285, E.294, L.296, K.308, P.309, I.310, Q.311, G.312, F.372, L.373, G.374, Q.375 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.312, B:G.312 Hydrophobic interactions: B:F.372 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.4: 18 residues within 4Å: Chain B: N.120 Chain C: R.247, N.249, D.250, R.283, I.285, T.287, E.294, L.296, K.308, P.309, I.310, Q.311, G.312, F.372, L.373, G.374, Q.375 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.372 Hydrogen bonds: C:G.312 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.6: 18 residues within 4Å: Chain C: N.119, N.120 Chain D: R.247, N.249, D.250, R.283, I.285, E.294, L.296, K.308, P.309, I.310, Q.311, G.312, F.372, L.373, G.374, Q.375 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:F.372 Hydrogen bonds: D:G.312 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.8: 19 residues within 4Å: Chain A: R.247, N.249, D.250, R.283, I.285, T.287, E.294, L.296, K.308, P.309, I.310, Q.311, G.312, F.372, L.373, G.374, Q.375 Chain D: N.119, N.120 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.372 Hydrogen bonds: A:G.312

3 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.3: 8 residues within 4Å: Chain B: N.65, W.357 Chain G: K.19, A.72, D.73, E.74, S.75, Y.80 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:K.19, G:E.74 NAG-NAG-BMA-MAN.5: 7 residues within 4Å: Chain C: N.65, W.357 Chain I: K.19, A.72, D.73, E.74, Y.80 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:K.19, I:E.74 NAG-NAG-BMA-MAN.7: 8 residues within 4Å: Chain D: N.65, W.357 Chain K: K.19, A.72, D.73, E.74, S.75, Y.80 3 PLIP interactions: 3 interactions with chain K Hydrogen bonds: K:K.19, K:A.72, K:E.74, K:S.75

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

NAG.9: 4 residues within 4Å: Chain A: N.2, F.3, N.5, N.154 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.2 Hydrogen bonds: A:N.2, A:F.3 NAG.11: 4 residues within 4Å: Chain B: N.2, F.3, N.5, N.154 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:N.2 Hydrogen bonds: B:N.2, B:F.3 NAG.13: 4 residues within 4Å: Chain C: N.2, F.3, N.5, N.154 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:N.2 Hydrogen bonds: C:F.3 NAG.15: 3 residues within 4Å: Chain D: F.3, N.5, N.154 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:F.3

4 x CA: CALCIUM ION(Non-covalent)

CA.10: 5 residues within 4Å: Chain A: D.213, G.217, D.244, N.266, G.267 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.213, A:G.217, A:N.266 CA.12: 4 residues within 4Å: Chain B: D.213, G.217, D.244, N.266 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:G.217, B:N.266 CA.14: 4 residues within 4Å: Chain C: D.213, G.217, D.244, N.266 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.213, C:G.217, C:N.266 CA.16: 6 residues within 4Å: Chain D: D.213, G.217, S.218, D.244, N.263, N.266 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.213, D:G.217, D:N.266

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jiang, H. et al., Structure-Based Modification of an Anti-neuraminidase Human Antibody Restores Protection Efficacy against the Drifted Influenza Virus. Mbio (2020)

Release Date

2020-12-02

Peptides

Neuraminidase: ABCD
Heavy chain of Z2B3 Fab: EGIK
Light chain of Z2B3 Fab: FHJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
H

G
E

I
J

K
M

F
L

H
F

J
K

L
N

Neuraminidase

Heavy chain of Z2B3 Fab

Light chain of Z2B3 Fab

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