SMTL ID : 6g01.1 (1 other biounit)

Complex of neuraminidase from H1N1 influenza virus with tamiphosphor monomethyl ester

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.61 Å

Oligo State

homo-tetramer

Ligands

4 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 1 residues within 4Å: Chain A: N.7 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 1 residues within 4Å: Chain B: N.7 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 1 residues within 4Å: Chain C: N.7 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 1 residues within 4Å: Chain D: N.7 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.2: 2 residues within 4Å: Chain A: K.3, N.154 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 2 residues within 4Å: Chain B: K.3, N.154 No protein-ligand interaction detected (PLIP)

8 x CA: CALCIUM ION(Non-covalent)

CA.3: 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.4 CA.4: 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.7, H2O.11 CA.13: 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.19 CA.14: 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.22, 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.34 CA.24: 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.36, H2O.43 CA.32: 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.50 CA.33: 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.52, H2O.59

4 x EEW: [(3~{R},4~{R},5~{S})-4-acetamido-5-azanyl-3-pentan-3-yloxy-cyclohexen-1-yl]-methoxy-phosphinic acid(Non-covalent)

EEW.5: 13 residues within 4Å: Chain A: R.37, E.38, D.70, R.71, W.98, R.144, S.166, E.196, E.197, R.212, N.214, R.287, Y.321 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.98, A:E.196 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:Y.321 Water bridges: A:R.75 EEW.15: 13 residues within 4Å: Chain B: R.37, E.38, D.70, R.71, 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:W.98, B:E.196 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:Y.321, B:Y.321 Water bridges: B:D.70 EEW.25: 13 residues within 4Å: Chain C: R.37, E.38, D.70, R.71, W.98, R.144, S.166, E.196, E.197, R.212, N.214, R.287, Y.321 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:W.98 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:Y.321 Water bridges: C:D.70, C:E.197 EEW.34: 13 residues within 4Å: Chain D: R.37, E.38, D.70, R.71, 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 D Hydrophobic interactions: D:W.98 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:Y.321, D:Y.321 Water bridges: D:R.75, D:E.197

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

NAG.6: 2 residues within 4Å: Chain A: N.65, I.355 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.355 Water bridges: A:N.65 NAG.16: 2 residues within 4Å: Chain B: N.65, I.355 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.355 Water bridges: B:N.65 NAG.26: 2 residues within 4Å: Chain C: K.3, N.154 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.3, C:N.154 NAG.35: 2 residues within 4Å: Chain D: K.3, N.154 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.3, D:N.154

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

EDO.7: 3 residues within 4Å: Chain A: V.13, W.277, W.294 No protein-ligand interaction detected (PLIP) EDO.8: 5 residues within 4Å: Chain A: N.65, G.66, K.69, S.72 Chain C: R.26 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:R.26, C:R.26, A:S.72 Water bridges: A:H.63, A:N.65 EDO.9: 7 residues within 4Å: Chain A: N.128, G.129, I.130 Chain C: Y.19, L.46, E.47, C.48 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:L.46, C:C.48, C:C.48 Water bridges: C:E.47 EDO.10: 1 residues within 4Å: Chain A: P.191 No protein-ligand interaction detected (PLIP) EDO.17: 3 residues within 4Å: Chain B: V.13, W.277, W.294 No protein-ligand interaction detected (PLIP) EDO.18: 5 residues within 4Å: Chain B: N.65, G.66, K.69, S.72 Chain D: R.26 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:S.72, D:R.26, D:R.26 Water bridges: B:H.63, B:N.65 EDO.19: 7 residues within 4Å: Chain B: N.128, G.129, I.130 Chain D: Y.19, L.46, E.47, C.48 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:L.46, D:C.48, D:C.48 EDO.20: 1 residues within 4Å: Chain B: P.191 No protein-ligand interaction detected (PLIP) EDO.27: 3 residues within 4Å: Chain C: P.12, V.13, W.294 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:V.13 EDO.28: 5 residues within 4Å: Chain A: Y.89, N.90, S.91, R.92 Chain C: E.84 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:Y.89, C:E.84 EDO.29: 2 residues within 4Å: Chain C: K.184, S.185 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.185 EDO.36: 3 residues within 4Å: Chain D: P.12, V.13, W.294 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:V.13 EDO.37: 5 residues within 4Å: Chain B: Y.89, N.90, S.91, R.92 Chain D: E.84 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:Y.89, D:E.84 EDO.38: 2 residues within 4Å: Chain D: K.184, S.185 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.185

2 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.22: 4 residues within 4Å: Chain C: K.62, N.65, I.355, I.386 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.31: 4 residues within 4Å: Chain D: K.62, N.65, I.355, I.386 No protein-ligand interaction detected (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
A

B
A

C
B

D
B

Neuraminidase

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