SMTL ID : 6d96.1 (1 other biounit)

Structure of influenza neuraminidase from strain A/BrevigMission/1/1918(H1N1) expressed in HEK-293E cells

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-tetramer

Ligands

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

NAG-NAG-FUC.1: 5 residues within 4Å: Chain B: N.170, S.172, K.192, E.194, Q.243 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.192, B:E.194 Water bridges: B:S.172 NAG-NAG-FUC.2: 3 residues within 4Å: Chain C: N.170, E.194, Q.243 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.192, C:E.194

1 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.3: 4 residues within 4Å: Chain D: N.170, S.172, K.192, E.194 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:G.171, D:S.172, D:S.172, D:K.192

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

NAG.4: 2 residues within 4Å: Chain A: N.81, T.83 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.81 NAG.5: 2 residues within 4Å: Chain A: N.23, S.24 No protein-ligand interaction detected (PLIP) NAG.6: 2 residues within 4Å: Chain A: N.170, Q.243 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.243 NAG.11: 2 residues within 4Å: Chain B: N.81, T.83 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.81, B:T.83 NAG.12: 1 residues within 4Å: Chain B: N.23 No protein-ligand interaction detected (PLIP) NAG.15: 2 residues within 4Å: Chain C: N.81, T.83 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.81 NAG.16: 2 residues within 4Å: Chain C: N.23, S.24 No protein-ligand interaction detected (PLIP) NAG.20: 2 residues within 4Å: Chain D: N.81, T.83 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.81 NAG.21: 1 residues within 4Å: Chain D: N.23 No protein-ligand interaction detected (PLIP)

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

CA.7: 5 residues within 4Å: Chain A: D.229, G.233, D.259, G.277, N.279 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.229, A:G.233, A:D.259, A:G.277, A:N.279, H2O.2 CA.8: 4 residues within 4Å: Chain A: D.311, N.313, D.319, S.321 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.311, A:D.311, A:D.319, H2O.3, H2O.5 CA.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.13: 6 residues within 4Å: Chain B: D.229, G.233, D.259, G.277, N.279, G.280 6 PLIP interactions: 5 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.229, B:G.233, B:D.259, B:G.277, B:N.279, H2O.9 CA.14: 4 residues within 4Å: Chain B: D.311, N.313, D.319, S.321 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.311, B:D.311, B:D.319, H2O.8, H2O.10 CA.17: 6 residues within 4Å: Chain C: D.229, G.233, D.259, G.277, N.279, G.280 6 PLIP interactions: 5 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.229, C:G.233, C:D.259, C:G.277, C:N.279, H2O.17 CA.18: 4 residues within 4Å: Chain C: D.311, N.313, D.319, S.321 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.311, C:D.311, C:D.319, H2O.15, H2O.18 CA.22: 6 residues within 4Å: Chain D: D.229, G.233, D.259, G.277, A.278, N.279 6 PLIP interactions: 5 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.229, D:G.233, D:D.259, D:G.277, D:N.279, H2O.22 CA.23: 4 residues within 4Å: Chain D: D.311, N.313, D.319, S.321 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.311, D:D.319, D:S.321, H2O.23, H2O.24

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 5 residues within 4Å: Chain A: P.28, I.29, Y.288, W.293, W.310 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.29, A:W.293 GOL.19: 5 residues within 4Å: Chain C: P.28, I.29, Y.288, W.293, W.310 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:I.29, C:W.293 GOL.24: 5 residues within 4Å: Chain D: P.28, I.29, Y.288, W.293, W.310 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:I.29, D:W.293

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Campbell, A.C. et al., Optimisation of neuraminidase expression by HEK-293E cells for use in structural biology. To Be Published

Release Date

2019-05-01

Peptides

Neuraminidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Neuraminidase

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