SMTL ID : 3ti5.1

Crystal structure of 2009 pandemic H1N1 neuraminidase complexed with Zanamivir

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

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.1: 4 residues within 4Å: Chain A: K.62, N.65, I.355, I.386 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.20: 4 residues within 4Å: Chain C: K.62, N.65, I.355, I.386 No protein-ligand interaction detected (PLIP)

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

NAG.2: 2 residues within 4Å: Chain A: A.5, N.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.7 NAG.10: 1 residues within 4Å: Chain B: N.65 No protein-ligand interaction detected (PLIP) NAG.11: 2 residues within 4Å: Chain B: A.5, N.7 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.7 NAG.21: 2 residues within 4Å: Chain C: A.5, N.7 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.7 NAG.29: 1 residues within 4Å: Chain D: N.65 No protein-ligand interaction detected (PLIP) NAG.30: 2 residues within 4Å: Chain D: A.5, N.7 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.7

10 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.3: 5 residues within 4Å: Chain A: D.213, G.217, D.243, G.261, N.263 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.2 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.2, H2O.3 CA.5: 1 residues within 4Å: Ligands: CA.24 No protein-ligand interaction detected (PLIP) CA.12: 5 residues within 4Å: Chain B: D.213, G.217, D.243, G.261, N.263 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.13: 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.17, H2O.18 CA.22: 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.31 CA.23: 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.32 CA.24: 1 residues within 4Å: Ligands: CA.5 No protein-ligand interaction detected (PLIP) CA.31: 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.45 CA.32: 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.47, H2O.47

4 x ZMR: ZANAMIVIR(Non-covalent)

ZMR.6: 16 residues within 4Å: Chain A: R.37, E.38, D.70, R.71, R.75, W.98, I.142, R.144, E.147, S.166, E.196, E.197, R.212, N.214, R.287, Y.321 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:W.98, A:I.142, A:R.144 Hydrogen bonds: A:R.71, A:W.98, A:W.98, A:R.144, A:E.197, A:R.212, A:R.212, A:Y.321 Water bridges: A:R.37, A:R.37, A:D.70, A:R.75, A:R.144, A:E.147, A:E.197 Salt bridges: A:R.37, A:E.38, A:D.70, A:E.147, A:R.212, A:R.287 ZMR.14: 16 residues within 4Å: Chain B: R.37, E.38, D.70, R.71, R.75, W.98, I.142, R.144, E.147, S.166, E.196, E.197, R.212, N.214, R.287, Y.321 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:W.98, B:I.142, B:R.144 Hydrogen bonds: B:R.71, B:W.98, B:W.98, B:R.144, B:E.197, B:R.212, B:R.212 Water bridges: B:R.37, B:D.70, B:R.75, B:R.144, B:E.147, B:E.197 Salt bridges: B:R.37, B:E.38, B:D.70, B:E.147, B:R.212, B:R.287 ZMR.25: 16 residues within 4Å: Chain C: R.37, E.38, D.70, R.71, R.75, W.98, I.142, R.144, E.147, S.166, E.196, E.197, R.212, N.214, R.287, Y.321 22 PLIP interactions: 22 interactions with chain C Hydrophobic interactions: C:W.98, C:I.142, C:R.144 Hydrogen bonds: C:R.71, C:W.98, C:W.98, C:R.144, C:E.197, C:R.212, C:R.212 Water bridges: C:R.37, C:R.37, C:D.70, C:R.75, C:R.144, C:E.197 Salt bridges: C:R.37, C:E.38, C:D.70, C:E.147, C:R.212, C:R.287 ZMR.33: 16 residues within 4Å: Chain D: R.37, E.38, D.70, R.71, R.75, W.98, I.142, R.144, E.147, S.166, E.196, E.197, R.212, N.214, R.287, Y.321 22 PLIP interactions: 22 interactions with chain D Hydrophobic interactions: D:W.98, D:I.142, D:R.144 Hydrogen bonds: D:R.71, D:W.98, D:W.98, D:R.144, D:E.197, D:R.212, D:R.212, D:Y.321 Water bridges: D:R.37, D:D.70, D:R.75, D:R.144, D:E.197 Salt bridges: D:R.37, D:E.38, D:D.70, D:E.147, D:R.212, D:R.287

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 8 residues within 4Å: Chain A: W.318, I.346, R.347, G.348, R.349, P.350, K.351, E.352 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.346, A:G.348, A:K.351, A:E.352, A:E.352 GOL.9: 5 residues within 4Å: Chain A: P.12, V.13, Y.272, W.277, W.294 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.13, A:Y.272 Water bridges: A:W.294 GOL.18: 6 residues within 4Å: Chain B: P.12, V.13, S.14, Y.272, W.277, W.294 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.13 Water bridges: B:W.294 GOL.26: 8 residues within 4Å: Chain C: W.318, I.346, R.347, G.348, R.349, P.350, K.351, E.352 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:I.346, C:G.348, C:K.351, C:E.352 GOL.28: 5 residues within 4Å: Chain C: P.12, V.13, Y.272, W.277, W.294 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:V.13, C:Y.272 Water bridges: C:W.294 GOL.37: 6 residues within 4Å: Chain D: P.12, V.13, S.14, Y.272, W.277, W.294 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:V.13 Water bridges: D:W.294

10 x ACT: ACETATE ION(Non-functional Binders)

ACT.8: 7 residues within 4Å: Chain A: Y.19, L.46, E.47, C.48 Chain D: N.128, G.129, I.130 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.47 Hydrogen bonds: A:Y.19, A:C.48 ACT.15: 6 residues within 4Å: Chain B: I.346, G.348, R.349, P.350, K.351, E.352 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:K.351 Hydrogen bonds: B:E.352 Water bridges: B:R.349 ACT.16: 4 residues within 4Å: Chain B: K.309, Q.310, D.311, G.373 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:D.311 Hydrogen bonds: B:K.309, B:D.311 Water bridges: B:G.373 Salt bridges: B:K.309 ACT.17: 6 residues within 4Å: Chain A: N.128, G.129 Chain B: Y.19, L.46, E.47, C.48 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:E.47 Hydrogen bonds: B:Y.19 ACT.19: 7 residues within 4Å: Chain B: S.14, G.15, I.308, K.309, Q.310, T.371, V.372 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.308 Hydrogen bonds: B:K.309, B:T.371 Water bridges: B:G.373, B:G.373 ACT.27: 7 residues within 4Å: Chain B: N.128, G.129, I.130 Chain C: Y.19, L.46, E.47, C.48 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:E.47 Hydrogen bonds: C:Y.19, C:Y.19, C:C.48 ACT.34: 6 residues within 4Å: Chain D: I.346, G.348, R.349, P.350, K.351, E.352 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:K.351 Water bridges: D:R.349 ACT.35: 4 residues within 4Å: Chain D: K.309, Q.310, D.311, G.373 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:D.311 Hydrogen bonds: D:K.309, D:D.311 Water bridges: D:G.373 Salt bridges: D:K.309 ACT.36: 6 residues within 4Å: Chain C: N.128, G.129 Chain D: Y.19, L.46, E.47, C.48 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:E.47 Hydrogen bonds: D:Y.19, D:Y.19 ACT.38: 7 residues within 4Å: Chain D: S.14, G.15, I.308, K.309, Q.310, T.371, V.372 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:I.308 Hydrogen bonds: D:K.309 Water bridges: D:G.373, D:G.373

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vavricka, C.J. et al., Structural and functional analysis of laninamivir and its octanoate prodrug reveals group specific mechanisms for influenza NA inhibition. Plos Pathog. (2011)

Release Date

2011-11-16

Peptides

Neuraminidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Neuraminidase

Related Entries With Identical Sequence