SMTL ID : 6g02.2 (1 other biounit)

Complex of neuraminidase from H1N1 influenza virus with tamiphosphor omega-azidohexyl ester

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

homo-tetramer

Ligands

8 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: D.213, G.217, D.243, G.261, N.263, G.264 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.213, A:G.217, A:D.243, A:G.261, A:N.263, H2O.1 CA.2: 4 residues within 4Å: Chain A: D.295, G.298, G.301, D.303 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.295, A:D.303, H2O.11 CA.12: 6 residues within 4Å: Chain B: D.213, G.217, D.243, G.261, N.263, G.264 6 PLIP interactions: 5 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.213, B:G.217, B:D.243, B:G.261, B:N.263, H2O.16 CA.13: 4 residues within 4Å: Chain B: D.295, G.298, G.301, D.303 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.295, B:D.303, H2O.27 CA.23: 6 residues within 4Å: Chain C: D.213, G.217, D.243, G.261, N.263, G.264 6 PLIP interactions: 5 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.213, C:G.217, C:D.243, C:G.261, C:N.263, H2O.32 CA.24: 4 residues within 4Å: Chain C: D.295, G.298, G.301, D.303 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.295, C:D.303, H2O.43 CA.34: 6 residues within 4Å: Chain D: D.213, G.217, D.243, G.261, N.263, G.264 6 PLIP interactions: 5 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.213, D:G.217, D:D.243, D:G.261, D:N.263, H2O.48 CA.35: 4 residues within 4Å: Chain D: D.295, G.298, G.301, D.303 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.295, D:D.303, H2O.58

4 x EF8: 6-[[(3~{R},4~{R},5~{S})-4-acetamido-5-azanyl-3-pentan-3-yloxy-cyclohexen-1-yl]-oxidanyl-phosphoryl]oxyhexylimino-azanylidene-azanium(Non-covalent)

EF8.3: 16 residues within 4Å: Chain A: R.37, E.38, I.68, D.70, R.71, W.98, R.144, S.166, E.196, E.197, R.212, N.214, R.287, Y.321, R.349, P.350 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:W.98, A:P.350 Hydrogen bonds: A:R.37, A:R.37, A:E.38, A:R.71, A:R.212, A:R.212, A:R.287, A:R.287, A:R.349, A:R.349 Water bridges: A:R.75, A:E.147 EF8.14: 16 residues within 4Å: Chain B: R.37, E.38, I.68, D.70, R.71, W.98, R.144, S.166, E.196, E.197, R.212, N.214, R.287, Y.321, R.349, P.350 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:W.98, B:P.350 Hydrogen bonds: B:R.37, B:R.37, B:E.38, B:R.71, B:R.212, B:R.212, B:R.287, B:R.287, B:R.349, B:R.349 Water bridges: B:R.75, B:E.147 EF8.25: 16 residues within 4Å: Chain C: R.37, E.38, I.68, D.70, R.71, W.98, R.144, S.166, E.196, E.197, R.212, N.214, R.287, Y.321, R.349, P.350 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:W.98, C:P.350 Hydrogen bonds: C:R.37, C:R.37, C:E.38, C:R.71, C:R.212, C:R.212, C:R.287, C:R.287, C:R.349, C:R.349 Water bridges: C:R.75, C:E.147 EF8.36: 16 residues within 4Å: Chain D: R.37, E.38, I.68, D.70, R.71, W.98, R.144, S.166, E.196, E.197, R.212, N.214, R.287, Y.321, R.349, P.350 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:W.98, D:P.350 Hydrogen bonds: D:R.37, D:R.37, D:E.38, D:R.71, D:R.212, D:R.212, D:R.287, D:R.287, D:R.349, D:R.349 Water bridges: D:R.75, D:E.147

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

NAG.4: 1 residues within 4Å: Chain A: N.7 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.7 NAG.5: 2 residues within 4Å: Chain A: N.65, I.355 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:I.355 Water bridges: A:N.65, D:E.381 NAG.6: 2 residues within 4Å: Chain A: N.305, F.306 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.306 Hydrogen bonds: A:N.305, A:F.306 NAG.15: 1 residues within 4Å: Chain B: N.7 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.7 NAG.16: 2 residues within 4Å: Chain B: N.65, I.355 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:I.355 Water bridges: B:N.65, C:E.381 NAG.17: 2 residues within 4Å: Chain B: N.305, F.306 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.306 Hydrogen bonds: B:N.305, B:F.306 NAG.26: 1 residues within 4Å: Chain C: N.7 1 PLIP interactions: 1 interactions with chain C Water bridges: C:N.7 NAG.27: 2 residues within 4Å: Chain C: N.65, I.355 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:I.355 Water bridges: C:N.65, A:E.381 NAG.28: 2 residues within 4Å: Chain C: N.305, F.306 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.306 Hydrogen bonds: C:N.305, C:F.306 NAG.37: 1 residues within 4Å: Chain D: N.7 1 PLIP interactions: 1 interactions with chain D Water bridges: D:N.7 NAG.38: 2 residues within 4Å: Chain D: N.65, I.355 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:I.355 Water bridges: D:N.65, B:E.381 NAG.39: 2 residues within 4Å: Chain D: N.305, F.306 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:F.306 Hydrogen bonds: D:N.305, D:F.306

20 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 4 residues within 4Å: Chain A: S.9, D.203, K.271, Y.272 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: K.271, G.273, N.274, T.300 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain A: N.65, G.66, T.67, K.69, S.72 Chain D: R.26 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: P.12, V.13, Y.272, W.277, W.294 Ligand excluded by PLIP EDO.11: 7 residues within 4Å: Chain A: Y.19, L.46, E.47, C.48, I.82 Chain C: N.128, G.129 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain B: S.9, D.203, K.271, Y.272 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain B: K.271, G.273, N.274, T.300 Ligand excluded by PLIP EDO.20: 6 residues within 4Å: Chain B: N.65, G.66, T.67, K.69, S.72 Chain C: R.26 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain B: P.12, V.13, Y.272, W.277, W.294 Ligand excluded by PLIP EDO.22: 7 residues within 4Å: Chain B: Y.19, L.46, E.47, C.48, I.82 Chain D: N.128, G.129 Ligand excluded by PLIP EDO.29: 4 residues within 4Å: Chain C: S.9, D.203, K.271, Y.272 Ligand excluded by PLIP EDO.30: 4 residues within 4Å: Chain C: K.271, G.273, N.274, T.300 Ligand excluded by PLIP EDO.31: 6 residues within 4Å: Chain A: R.26 Chain C: N.65, G.66, T.67, K.69, S.72 Ligand excluded by PLIP EDO.32: 5 residues within 4Å: Chain C: P.12, V.13, Y.272, W.277, W.294 Ligand excluded by PLIP EDO.33: 7 residues within 4Å: Chain B: N.128, G.129 Chain C: Y.19, L.46, E.47, C.48, I.82 Ligand excluded by PLIP EDO.40: 4 residues within 4Å: Chain D: S.9, D.203, K.271, Y.272 Ligand excluded by PLIP EDO.41: 4 residues within 4Å: Chain D: K.271, G.273, N.274, T.300 Ligand excluded by PLIP EDO.42: 6 residues within 4Å: Chain B: R.26 Chain D: N.65, G.66, T.67, K.69, S.72 Ligand excluded by PLIP EDO.43: 5 residues within 4Å: Chain D: P.12, V.13, Y.272, W.277, W.294 Ligand excluded by PLIP EDO.44: 7 residues within 4Å: Chain A: N.128, G.129 Chain D: Y.19, L.46, E.47, C.48, I.82 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kozisek, M. et al., DNA-linked inhibitor antibody assay (DIANA) as a new method for screening influenza neuraminidase inhibitors. Biochem. J. (2018)

Release Date

2019-01-23

Peptides

Neuraminidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

C
B

D
B

Neuraminidase

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