SMTL ID : 6lxi.1 (1 other biounit)

Crystal structure of Z2B3 Fab in complex with influenza virus neuraminidase from A/Brevig Mission/1/1918 (H1N1)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-4-4-4-mer

Ligands

4 x NAG- NAG- BMA- MAN- FUC: alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-FUC.1: 11 residues within 4Å: Chain A: N.146, K.150, Q.430, I.436 Chain B: K.19, P.53, V.54, A.72, D.73, E.74, S.75 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.150, A:K.150, A:Q.430, B:V.54, B:Y.80, B:E.74 Water bridges: B:T.71 NAG-NAG-BMA-MAN-FUC.4: 11 residues within 4Å: Chain D: N.146, K.150, Q.430, I.436 Chain E: K.19, P.53, V.54, A.72, D.73, E.74, S.75 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:K.150, D:K.150, D:Q.430, E:V.54, E:Y.80, E:E.74 Water bridges: E:T.71 NAG-NAG-BMA-MAN-FUC.7: 11 residues within 4Å: Chain G: N.146, K.150, Q.430, I.436 Chain H: K.19, P.53, V.54, A.72, D.73, E.74, S.75 4 PLIP interactions: 1 interactions with chain H, 3 interactions with chain G Hydrogen bonds: H:V.54, G:K.150, G:K.150, G:Q.430, H:Y.80, H:E.74 Water bridges: H:T.71 NAG-NAG-BMA-MAN-FUC.10: 11 residues within 4Å: Chain J: N.146, K.150, Q.430, I.436 Chain K: K.19, P.53, V.54, A.72, D.73, E.74, S.75 4 PLIP interactions: 3 interactions with chain J, 1 interactions with chain K Hydrogen bonds: J:K.150, J:K.150, J:Q.430, K:V.54, K:Y.80, K:E.74 Water bridges: K:T.71

8 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: D.294, G.298, D.324, G.342, N.344, G.345 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.294, A:G.298, A:D.324, A:G.342, A:N.344, H2O.3 CA.3: 4 residues within 4Å: Chain A: D.376, N.378, D.384, S.386 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.376, A:D.384, A:S.386, H2O.1, H2O.2 CA.5: 6 residues within 4Å: Chain D: D.294, G.298, D.324, G.342, N.344, G.345 6 PLIP interactions: 5 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.294, D:G.298, D:D.324, D:G.342, D:N.344, H2O.16 CA.6: 4 residues within 4Å: Chain D: D.376, N.378, D.384, S.386 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.376, D:D.384, D:S.386, H2O.14, H2O.15 CA.8: 6 residues within 4Å: Chain G: D.294, G.298, D.324, G.342, N.344, G.345 6 PLIP interactions: 5 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:D.294, G:G.298, G:D.324, G:G.342, G:N.344, H2O.29 CA.9: 4 residues within 4Å: Chain G: D.376, N.378, D.384, S.386 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:D.376, G:D.384, G:S.386, H2O.27, H2O.28 CA.11: 6 residues within 4Å: Chain J: D.294, G.298, D.324, G.342, N.344, G.345 6 PLIP interactions: 5 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:D.294, J:G.298, J:D.324, J:G.342, J:N.344, H2O.42 CA.12: 4 residues within 4Å: Chain J: D.376, N.378, D.384, S.386 5 PLIP interactions: 3 interactions with chain J, 2 Ligand-Water interactions Metal complexes: J:D.376, J:D.384, J:S.386, H2O.40, H2O.41

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: ADGJ
Heavy chain of Z2B3 Fab: BEHK
Light chain of Z2B3 Fab: CFIL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
A

G
A

J
A

B
H

E
H

H
H

K
H

C
L

F
L

I
L

L
L

Neuraminidase

Heavy chain of Z2B3 Fab

Light chain of Z2B3 Fab

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