SMTL ID : 4i00.1

Crystal structure of influenza A neuraminidase N3-H274Y complexed with zanamivir

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

8 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: 3 residues within 4Å: Chain A: N.65, S.356, K.388 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.2: 5 residues within 4Å: Chain A: P.7, D.154, N.226, N.227, E.228 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.206 NAG-NAG-FUC.6: 3 residues within 4Å: Chain B: N.65, S.356, K.388 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.7: 5 residues within 4Å: Chain B: P.7, D.154, N.226, N.227, E.228 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.206 NAG-NAG-FUC.11: 3 residues within 4Å: Chain C: N.65, S.356, K.388 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.12: 5 residues within 4Å: Chain C: P.7, D.154, N.226, N.227, E.228 1 PLIP interactions: 1 interactions with chain C Water bridges: C:D.206 NAG-NAG-FUC.16: 3 residues within 4Å: Chain D: N.65, S.356, K.388 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.17: 5 residues within 4Å: Chain D: P.7, D.154, N.226, N.227, E.228 1 PLIP interactions: 1 interactions with chain D Water bridges: D:D.206

8 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: D.213, G.217, D.243, G.263, G.266 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.213, A:G.217, A:D.243, A:G.263, H2O.2 CA.4: 7 residues within 4Å: Chain A: D.32 Chain B: D.32 Chain C: D.32 Chain D: D.32 Ligands: CA.9, CA.14, CA.19 No protein-ligand interaction detected (PLIP) CA.8: 5 residues within 4Å: Chain B: D.213, G.217, D.243, G.263, G.266 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.213, B:G.217, B:D.243, B:G.263, H2O.18 CA.9: 7 residues within 4Å: Chain A: D.32 Chain B: D.32 Chain C: D.32 Chain D: D.32 Ligands: CA.4, CA.14, CA.19 No protein-ligand interaction detected (PLIP) CA.13: 5 residues within 4Å: Chain C: D.213, G.217, D.243, G.263, G.266 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.213, C:G.217, C:D.243, C:G.263, H2O.33 CA.14: 7 residues within 4Å: Chain A: D.32 Chain B: D.32 Chain C: D.32 Chain D: D.32 Ligands: CA.4, CA.9, CA.19 No protein-ligand interaction detected (PLIP) CA.18: 5 residues within 4Å: Chain D: D.213, G.217, D.243, G.263, G.266 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.213, D:G.217, D:D.243, D:G.263, H2O.49 CA.19: 7 residues within 4Å: Chain A: D.32 Chain B: D.32 Chain C: D.32 Chain D: D.32 Ligands: CA.4, CA.9, CA.14 No protein-ligand interaction detected (PLIP)

4 x ZMR: ZANAMIVIR(Non-covalent)

ZMR.5: 17 residues within 4Å: Chain A: R.37, E.38, L.53, D.70, R.71, R.75, W.98, I.142, R.144, E.147, A.166, E.197, E.198, R.212, N.214, R.289, Y.324 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:W.98, A:I.142, A:R.144 Hydrogen bonds: A:R.71, A:W.98, A:W.98, A:R.144, A:E.198, A:R.212, A:N.214 Water bridges: A:R.37, A:D.70, A:R.75, A:R.75, A:R.144, A:E.147, A:E.198, A:R.212, A:R.212 Salt bridges: A:R.37, A:E.38, A:D.70, A:E.147, A:R.212, A:R.289 ZMR.10: 17 residues within 4Å: Chain B: R.37, E.38, L.53, D.70, R.71, R.75, W.98, I.142, R.144, E.147, A.166, E.197, E.198, R.212, N.214, R.289, Y.324 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:W.98, B:I.142, B:R.144 Hydrogen bonds: B:R.71, B:W.98, B:W.98, B:R.144, B:E.198, B:R.212, B:N.214 Water bridges: B:R.37, B:D.70, B:R.75, B:R.75, B:R.144, B:E.147, B:E.198, B:R.212, B:R.212 Salt bridges: B:R.37, B:E.38, B:D.70, B:E.147, B:R.212, B:R.289 ZMR.15: 17 residues within 4Å: Chain C: R.37, E.38, L.53, D.70, R.71, R.75, W.98, I.142, R.144, E.147, A.166, E.197, E.198, R.212, N.214, R.289, Y.324 25 PLIP interactions: 25 interactions with chain C Hydrophobic interactions: C:W.98, C:I.142, C:R.144 Hydrogen bonds: C:R.71, C:W.98, C:W.98, C:R.144, C:E.198, C:R.212, C:N.214 Water bridges: C:R.37, C:D.70, C:R.75, C:R.75, C:R.144, C:E.147, C:E.198, C:R.212, C:R.212 Salt bridges: C:R.37, C:E.38, C:D.70, C:E.147, C:R.212, C:R.289 ZMR.20: 17 residues within 4Å: Chain D: R.37, E.38, L.53, D.70, R.71, R.75, W.98, I.142, R.144, E.147, A.166, E.197, E.198, R.212, N.214, R.289, Y.324 25 PLIP interactions: 25 interactions with chain D Hydrophobic interactions: D:W.98, D:I.142, D:R.144 Hydrogen bonds: D:R.71, D:W.98, D:W.98, D:R.144, D:E.198, D:R.212, D:N.214 Water bridges: D:R.37, D:D.70, D:R.75, D:R.75, D:R.144, D:E.147, D:E.198, D:R.212, D:R.212 Salt bridges: D:R.37, D:E.38, D:D.70, D:E.147, D:R.212, D:R.289

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, Q. et al., Functional and structural analysis of influenza virus neuraminidase N3 offers further insight into the mechanisms of oseltamivir resistance. J.Virol. (2013)

Release Date

2013-11-13

Peptides

Neuraminidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Neuraminidase

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