SMTL ID : 6lxk.1

Crystal structure of Z2B3 D102R Fab in complex with influenza virus neuraminidase from A/Serbia/NS-601/2014 (H1N1)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.61 Å

Oligo State

hetero-4-3-3-mer

Ligands

4 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: 5 residues within 4Å: Chain A: N.146 Chain B: A.72, D.73, E.74, Y.80 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.73, B:E.74 NAG-NAG-BMA.2: 1 residues within 4Å: Chain D: N.146 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 5 residues within 4Å: Chain E: N.146 Chain I: A.72, D.73, E.74, Y.80 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:E.74 NAG-NAG-BMA.4: 4 residues within 4Å: Chain F: N.146 Chain G: A.72, D.73, E.74 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:E.74

8 x CA: CALCIUM ION(Non-covalent)

CA.5: 7 residues within 4Å: Chain A: D.294, G.298, D.324, G.342, A.343, N.344, G.345 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.294, A:G.298, A:D.324, A:A.343 CA.6: 4 residues within 4Å: Chain A: D.376, N.378, D.384, K.386 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.376, A:D.384, A:K.386 CA.7: 7 residues within 4Å: Chain D: D.294, G.298, D.324, G.342, A.343, N.344, G.345 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.294, D:G.298, D:D.324, D:G.342, D:A.343 CA.8: 4 residues within 4Å: Chain D: D.376, N.378, D.384, K.386 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.376, D:D.384, D:K.386 CA.9: 7 residues within 4Å: Chain E: D.294, G.298, D.324, G.342, A.343, N.344, G.345 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.294, E:G.298, E:D.324, E:A.343 CA.10: 4 residues within 4Å: Chain E: D.376, N.378, D.384, K.386 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:D.376, E:D.384, E:K.386 CA.11: 7 residues within 4Å: Chain F: D.294, G.298, D.324, G.342, A.343, N.344, G.345 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.294, F:G.298, F:D.324, F:A.343 CA.12: 4 residues within 4Å: Chain F: D.376, N.378, D.384, K.386 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:D.376, F:D.384, F:K.386

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: ADEF
Heavy chain of Z2B3-D102R Fab: BGI
Light chain of Z2B3-D102R Fab: CHJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
B

E
C

F
D

B
H

G
E

I
J

C
L

H
F

J
K

Neuraminidase

Heavy chain of Z2B3-D102R Fab

Light chain of Z2B3-D102R Fab

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