SMTL ID : 6hp0.1

Complex of Neuraminidase from H1N1 Influenza Virus in Complex with Oseltamivir Triazol Derivative

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

homo-tetramer

Ligands

3 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: 4 residues within 4Å: Chain A: K.3, N.7, N.154 Ligands: NAG.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.3 NAG-NAG-FUC.3: 5 residues within 4Å: Chain B: K.3, A.5, N.7, N.154 Ligands: NAG.29 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.3 NAG-NAG-FUC.4: 5 residues within 4Å: Chain C: K.3, A.5, N.7, N.154 Ligands: NAG.39 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:A.5 Hydrogen bonds: C:K.3

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

NAG-FUC.2: 3 residues within 4Å: Chain A: N.65, I.355 Chain B: E.381 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:E.381, A:N.65 Water bridges: B:E.381, A:R.349 Hydrophobic interactions: A:I.355 NAG-FUC.6: 5 residues within 4Å: Chain D: K.3, A.5, N.7, N.154 Ligands: NAG.47 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.3, D:K.3

1 x NAG- NAG- BMA- MAN- MAN- FUC: alpha-D-mannopyranose-(1-3)-[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-MAN-FUC.5: 3 residues within 4Å: Chain C: N.65, I.355 Chain D: E.381 No protein-ligand interaction detected (PLIP)

8 x CA: CALCIUM ION(Non-covalent)

CA.7: 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.3 CA.8: 4 residues within 4Å: Chain A: D.295, N.297, D.303, N.305 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.295, A:D.303, A:N.305, H2O.5, H2O.6 CA.25: 7 residues within 4Å: Chain B: D.213, G.217, D.243, G.261, A.262, 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.15 CA.26: 4 residues within 4Å: Chain B: D.295, N.297, D.303, N.305 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.295, B:D.303, B:N.305, H2O.14, H2O.16 CA.36: 5 residues within 4Å: Chain C: D.213, G.217, D.243, G.261, N.263 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.29 CA.37: 4 residues within 4Å: Chain C: D.295, N.297, D.303, N.305 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.295, C:D.303, C:N.305, H2O.32, H2O.35 CA.43: 5 residues within 4Å: Chain D: D.213, G.217, D.243, G.261, N.263 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.42 CA.44: 4 residues within 4Å: Chain D: D.295, N.297, D.303, N.305 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.295, D:D.303, D:N.305, H2O.43, H2O.43

4 x GJT: (3~{R},4~{R},5~{S})-4-acetamido-5-[4-(hydroxymethyl)-1,2,3-triazol-1-yl]-3-pentan-3-yloxy-cyclohexene-1-carboxylic acid(Non-covalent)

GJT.9: 17 residues within 4Å: Chain A: R.37, E.38, L.53, I.68, K.69, D.70, R.71, R.75, W.98, R.144, S.166, E.196, E.197, R.212, N.214, R.287, Y.321 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:E.196, A:N.214 Hydrogen bonds: A:D.70, A:R.71, A:R.75, A:Y.321 Water bridges: A:R.37, A:E.38, A:E.38, A:S.99, A:E.197, A:R.212 Salt bridges: A:R.37, A:R.212, A:R.287 GJT.27: 15 residues within 4Å: Chain B: R.37, E.38, K.69, D.70, R.71, R.75, W.98, R.144, S.166, E.196, E.197, R.212, N.214, R.287, Y.321 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:E.196, B:N.214 Hydrogen bonds: B:R.37, B:D.70, B:R.71, B:R.75, B:Y.321 Water bridges: B:E.38, B:E.38, B:S.99, B:E.197 Salt bridges: B:R.212, B:R.287 GJT.38: 16 residues within 4Å: Chain C: R.37, E.38, L.53, K.69, D.70, R.71, R.75, W.98, R.144, S.166, E.196, E.197, R.212, N.214, R.287, Y.321 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:E.196 Hydrogen bonds: C:R.37, C:D.70, C:R.71, C:R.75, C:Y.321 Water bridges: C:E.38, C:E.38, C:S.99, C:E.197, C:N.263 Salt bridges: C:R.212, C:R.287 GJT.45: 17 residues within 4Å: Chain D: R.37, E.38, L.53, I.68, K.69, D.70, R.71, R.75, W.98, R.144, S.166, E.196, E.197, R.212, N.214, R.287, Y.321 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:W.98, D:E.196 Hydrogen bonds: D:D.70, D:R.71, D:R.75, D:Y.321 Water bridges: D:S.99, D:E.197 Salt bridges: D:R.37, D:R.212, D:R.287

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

NAG.10: 3 residues within 4Å: Chain A: K.3, N.154 Ligands: NAG-NAG-FUC.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.3, A:N.154 Water bridges: A:Q.227 NAG.28: 2 residues within 4Å: Chain B: N.65, I.355 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.355 Hydrogen bonds: B:N.65 NAG.29: 3 residues within 4Å: Chain B: K.3, N.154 Ligands: NAG-NAG-FUC.3 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.3 Water bridges: B:N.154 NAG.39: 3 residues within 4Å: Chain C: K.3, N.154 Ligands: NAG-NAG-FUC.4 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.154 Water bridges: C:Q.227 NAG.46: 2 residues within 4Å: Chain D: N.65, R.349 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.65, D:R.349 NAG.47: 3 residues within 4Å: Chain D: K.3, N.154 Ligands: NAG-FUC.6 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.3, D:N.154

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

EDO.11: 4 residues within 4Å: Chain A: C.11, P.12, R.338, N.368 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain A: P.12, V.13, Y.272, W.277 Ligand excluded by PLIP EDO.13: 3 residues within 4Å: Chain A: P.12, D.335, C.336 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain A: R.246, N.248, D.249, R.280, K.282, I.284 Ligand excluded by PLIP EDO.15: 1 residues within 4Å: Chain A: K.282 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain A: S.286, R.287, P.350, K.351 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain A: W.294, P.296, S.307, I.308 Ligand excluded by PLIP EDO.18: 2 residues within 4Å: Chain A: N.353, T.354 Ligand excluded by PLIP EDO.19: 1 residues within 4Å: Ligands: EDO.20 Ligand excluded by PLIP EDO.20: 1 residues within 4Å: Ligands: EDO.19 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain A: K.184, V.186, N.228, L.229, E.230 Ligand excluded by PLIP EDO.22: 2 residues within 4Å: Chain A: P.191, Y.193 Ligand excluded by PLIP EDO.23: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.24: 4 residues within 4Å: Chain A: D.311, G.314, W.374, S.375 Ligand excluded by PLIP EDO.30: 3 residues within 4Å: Chain B: P.165, N.167, G.168 Ligand excluded by PLIP EDO.31: 5 residues within 4Å: Chain A: N.128, I.130 Chain B: Y.19, E.47, C.48 Ligand excluded by PLIP EDO.32: 1 residues within 4Å: Chain B: N.305 Ligand excluded by PLIP EDO.33: 4 residues within 4Å: Chain B: P.73, Y.74 Chain C: E.317, P.377 Ligand excluded by PLIP EDO.34: 1 residues within 4Å: Chain B: T.251 Ligand excluded by PLIP EDO.35: 3 residues within 4Å: Chain B: Y.272, G.273, N.274 Ligand excluded by PLIP EDO.40: 4 residues within 4Å: Chain C: C.11, P.12, R.338, N.368 Ligand excluded by PLIP EDO.41: 9 residues within 4Å: Chain C: W.318, I.346, R.347, G.348, R.349, P.350, K.351, E.352, T.357 Ligand excluded by PLIP EDO.42: 4 residues within 4Å: Chain C: W.294, P.296, S.307, I.308 Ligand excluded by PLIP EDO.48: 1 residues within 4Å: Chain D: N.128 Ligand excluded by PLIP EDO.49: 7 residues within 4Å: Chain C: Y.89, N.90, S.91, R.92 Chain D: P.81, E.84, N.90 Ligand excluded by PLIP EDO.50: 7 residues within 4Å: Chain C: N.128, G.129, I.130 Chain D: Y.19, L.46, E.47, C.48 Ligand excluded by PLIP EDO.51: 5 residues within 4Å: Chain D: D.118, N.119, N.140, N.141, I.142 Ligand excluded by PLIP EDO.52: 1 residues within 4Å: Chain D: N.305 Ligand excluded by PLIP EDO.53: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.54: 5 residues within 4Å: Chain D: N.316, E.317, W.318, R.347, E.352 4 PLIP interactions: 4 interactions with chain D Water bridges: D:R.347, D:R.347, D:E.352, D:A.380

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zima, V. et al., Investigation of flexibility of neuraminidase 150-loop using tamiflu derivatives in influenza A viruses H1N1 and H5N1. Bioorg.Med.Chem. (2019)

Release Date

2019-09-11

Peptides

Neuraminidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Neuraminidase

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