SMTL ID : 1iny.1

A SIALIC ACID DERIVED PHOSPHONATE ANALOG INHIBITS DIFFERENT STRAINS OF INFLUENZA VIRUS NEURAMINIDASE WITH DIFFERENT EFFICIENCIES

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

4 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN-MAN-MAN.1: 22 residues within 4Å: Chain A: N.119, N.120, R.140 Chain B: V.241, R.247, N.249, D.250, R.283, I.285, I.287, E.294, L.296, K.308, P.309, T.310, Q.311, G.312, Q.313, F.372, L.373, G.374, Q.375 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.312, B:Q.375 NAG-NAG-BMA-MAN-MAN-MAN-MAN.6: 22 residues within 4Å: Chain B: N.119, N.120, R.140 Chain D: V.241, R.247, N.249, D.250, R.283, I.285, I.287, E.294, L.296, K.308, P.309, T.310, Q.311, G.312, Q.313, F.372, L.373, G.374, Q.375 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.312, D:Q.375 NAG-NAG-BMA-MAN-MAN-MAN-MAN.11: 22 residues within 4Å: Chain A: V.241, R.247, N.249, D.250, R.283, I.285, I.287, E.294, L.296, K.308, P.309, T.310, Q.311, G.312, Q.313, F.372, L.373, G.374, Q.375 Chain C: N.119, N.120, R.140 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.312, A:Q.375 NAG-NAG-BMA-MAN-MAN-MAN-MAN.16: 22 residues within 4Å: Chain C: V.241, R.247, N.249, D.250, R.283, I.285, I.287, E.294, L.296, K.308, P.309, T.310, Q.311, G.312, Q.313, F.372, L.373, G.374, Q.375 Chain D: N.119, N.120, R.140 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.312, C:Q.375

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

NAG.2: 5 residues within 4Å: Chain A: D.2, F.3, N.4, N.5, N.154 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.3 NAG.3: 2 residues within 4Å: Chain A: N.65, W.357 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.65 NAG.7: 5 residues within 4Å: Chain B: D.2, F.3, N.4, N.5, N.154 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.3 NAG.8: 2 residues within 4Å: Chain B: N.65, W.357 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.65 NAG.12: 5 residues within 4Å: Chain C: D.2, F.3, N.4, N.5, N.154 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:F.3 NAG.13: 2 residues within 4Å: Chain C: N.65, W.357 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.65 NAG.17: 5 residues within 4Å: Chain D: D.2, F.3, N.4, N.5, N.154 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:F.3 NAG.18: 2 residues within 4Å: Chain D: N.65, W.357 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.65

4 x CA: CALCIUM ION(Non-covalent)

CA.4: 4 residues within 4Å: Chain A: D.213, G.217, D.244, N.266 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.213, A:G.217, A:D.244, A:N.266, H2O.1 CA.9: 4 residues within 4Å: Chain B: D.213, G.217, D.244, N.266 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.213, B:G.217, B:D.244, B:N.266, H2O.3 CA.14: 4 residues within 4Å: Chain C: D.213, G.217, D.244, N.266 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.213, C:G.217, C:D.244, C:N.266, H2O.5 CA.19: 4 residues within 4Å: Chain D: D.213, G.217, D.244, N.266 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.213, D:G.217, D:D.244, D:N.266, H2O.7

4 x EQP: (1R)-4-acetamido-1,5-anhydro-2,4-dideoxy-1-phosphono-D-glycero-D-galacto-octitol(Non-covalent)

EQP.5: 17 residues within 4Å: Chain A: R.37, E.38, D.70, R.71, R.75, W.98, S.99, I.142, R.144, E.147, A.166, E.196, E.197, R.212, N.214, R.290, Y.324 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:I.142 Hydrogen bonds: A:R.37, A:R.37, A:R.71, A:R.71, A:E.196, A:R.212, A:R.290, A:R.290, A:Y.324 Water bridges: A:E.38, A:E.38, A:E.197, A:E.197 EQP.10: 17 residues within 4Å: Chain B: R.37, E.38, D.70, R.71, R.75, W.98, S.99, I.142, R.144, E.147, A.166, E.196, E.197, R.212, N.214, R.290, Y.324 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:I.142 Hydrogen bonds: B:R.37, B:R.37, B:R.71, B:R.71, B:E.196, B:R.212, B:R.290, B:R.290, B:Y.324 Water bridges: B:E.38, B:E.38, B:E.197, B:E.197 EQP.15: 17 residues within 4Å: Chain C: R.37, E.38, D.70, R.71, R.75, W.98, S.99, I.142, R.144, E.147, A.166, E.196, E.197, R.212, N.214, R.290, Y.324 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:I.142 Hydrogen bonds: C:R.37, C:R.37, C:R.71, C:R.71, C:E.196, C:R.212, C:R.290, C:R.290, C:Y.324 Water bridges: C:E.38, C:E.38, C:E.197, C:E.197 EQP.20: 17 residues within 4Å: Chain D: R.37, E.38, D.70, R.71, R.75, W.98, S.99, I.142, R.144, E.147, A.166, E.196, E.197, R.212, N.214, R.290, Y.324 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:I.142 Hydrogen bonds: D:R.37, D:R.37, D:R.71, D:R.71, D:E.196, D:R.212, D:R.290, D:R.290, D:Y.324 Water bridges: D:E.38, D:E.38, D:E.197, D:E.197

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

White, C.L. et al., A sialic acid-derived phosphonate analog inhibits different strains of influenza virus neuraminidase with different efficiencies. J.Mol.Biol. (1995)

Release Date

1995-02-07

Peptides

INFLUENZA A SUBTYPE N9 NEURAMINIDASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

INFLUENZA A SUBTYPE N9 NEURAMINIDASE