SMTL ID : 1inv.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: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 6 residues within 4Å: Chain A: Y.6, P.7, R.8, L.9, N.208, R.280 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.7 NAG.5: 6 residues within 4Å: Chain B: Y.6, P.7, R.8, L.9, N.208, R.280 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.7 NAG.9: 6 residues within 4Å: Chain C: Y.6, P.7, R.8, L.9, N.208, R.280 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:P.7 NAG.13: 6 residues within 4Å: Chain D: Y.6, P.7, R.8, L.9, N.208, R.280 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:P.7

8 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: D.217, T.221, D.248, W.268, G.270 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.217, A:T.221, A:D.248, H2O.1, H2O.1 CA.3: 7 residues within 4Å: Chain A: E.92 Chain B: E.92 Chain C: E.92 Chain D: E.92 Ligands: CA.7, CA.11, CA.15 4 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C Metal complexes: D:E.92, A:E.92, B:E.92, C:E.92 CA.6: 5 residues within 4Å: Chain B: D.217, T.221, D.248, W.268, G.270 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.217, B:T.221, B:D.248, H2O.5, H2O.5 CA.7: 7 residues within 4Å: Chain A: E.92 Chain B: E.92 Chain C: E.92 Chain D: E.92 Ligands: CA.3, CA.11, CA.15 4 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C Metal complexes: D:E.92, A:E.92, B:E.92, C:E.92 CA.10: 5 residues within 4Å: Chain C: D.217, T.221, D.248, W.268, G.270 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.217, C:T.221, C:D.248, H2O.10, H2O.10 CA.11: 7 residues within 4Å: Chain A: E.92 Chain B: E.92 Chain C: E.92 Chain D: E.92 Ligands: CA.3, CA.7, CA.15 4 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C Metal complexes: D:E.92, A:E.92, B:E.92, C:E.92 CA.14: 5 residues within 4Å: Chain D: D.217, T.221, D.248, W.268, G.270 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.217, D:T.221, D:D.248, H2O.14, H2O.14 CA.15: 7 residues within 4Å: Chain A: E.92 Chain B: E.92 Chain C: E.92 Chain D: E.92 Ligands: CA.3, CA.7, CA.11 4 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C Metal complexes: D:E.92, A:E.92, B:E.92, C:E.92

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

EQP.4: 18 residues within 4Å: Chain A: R.40, E.41, D.73, R.74, R.78, W.101, S.102, I.145, R.147, E.150, A.169, H.197, E.199, E.200, R.216, N.218, R.298, Y.333 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:W.101, A:R.147 Hydrogen bonds: A:R.40, A:R.40, A:D.73, A:R.74, A:E.199, A:R.216, A:R.216, A:R.298, A:R.298 Water bridges: A:D.73, A:R.147, A:R.147, A:E.150, A:E.200 EQP.8: 18 residues within 4Å: Chain B: R.40, E.41, D.73, R.74, R.78, W.101, S.102, I.145, R.147, E.150, A.169, H.197, E.199, E.200, R.216, N.218, R.298, Y.333 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:W.101, B:R.147 Hydrogen bonds: B:R.40, B:R.40, B:D.73, B:R.74, B:E.199, B:R.216, B:R.216, B:R.298, B:R.298 Water bridges: B:D.73, B:R.147, B:R.147, B:E.150, B:E.200 EQP.12: 18 residues within 4Å: Chain C: R.40, E.41, D.73, R.74, R.78, W.101, S.102, I.145, R.147, E.150, A.169, H.197, E.199, E.200, R.216, N.218, R.298, Y.333 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:W.101, C:R.147 Hydrogen bonds: C:R.40, C:R.40, C:D.73, C:R.74, C:E.199, C:R.216, C:R.216, C:R.298, C:R.298 Water bridges: C:D.73, C:R.147, C:R.147, C:E.150, C:E.200 EQP.16: 18 residues within 4Å: Chain D: R.40, E.41, D.73, R.74, R.78, W.101, S.102, I.145, R.147, E.150, A.169, H.197, E.199, E.200, R.216, N.218, R.298, Y.333 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:W.101, D:R.147 Hydrogen bonds: D:R.40, D:R.40, D:D.73, D:R.74, D:E.199, D:R.216, D:R.216, D:R.298, D:R.298 Water bridges: D:D.73, D:R.147, D:R.147, D:E.150, D:E.200

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 VIRUS B/LEE/40 NEURAMINIDASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

INFLUENZA VIRUS B/LEE/40 NEURAMINIDASE

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