SMTL ID : 6hg5.1

Influenza A virus N6 neuraminidase complex with Oseltamivir (Duck/England/56).

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 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: 3 residues within 4Å: Chain A: N.65, L.358 Chain C: Y.387 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: Y.387 Chain B: R.62, N.65, L.358 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain C: N.65, L.358 Chain D: Y.387 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: Y.387 Chain D: N.65, L.358 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[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-MAN-MAN-MAN.2: 18 residues within 4Å: Chain A: N.119, N.120 Chain C: N.14, S.15, D.250, R.284, E.295, L.297, P.310, I.311, S.312, N.313, Q.314, V.315, R.373, L.374, G.375, S.376 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.313, C:N.313, C:N.313, C:N.313, C:R.373, C:N.313 NAG-NAG-BMA-MAN-MAN-MAN-MAN.4: 18 residues within 4Å: Chain A: N.14, S.15, D.250, R.284, I.286, E.295, L.297, P.310, I.311, S.312, N.313, V.315, R.373, L.374, G.375, S.376 Chain B: N.119, N.120 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.313, A:N.313, A:N.313 Water bridges: A:R.373

2 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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.6: 17 residues within 4Å: Chain C: N.119, N.120 Chain D: N.14, D.250, R.284, I.286, E.295, L.297, P.310, I.311, S.312, N.313, Q.314, V.315, L.374, G.375, S.376 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:N.313, D:N.313, D:N.313, D:N.313, D:N.313, D:R.284, D:R.284 Water bridges: D:D.250, D:R.284, D:E.295 NAG-NAG-BMA-MAN-MAN-MAN.8: 17 residues within 4Å: Chain B: N.14, D.250, R.284, I.286, E.295, L.297, P.310, I.311, S.312, N.313, Q.314, V.315, L.374, G.375, S.376 Chain D: N.119, N.120 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.313, B:N.313, B:N.313, B:N.313, B:N.313, B:D.250, B:D.250, B:R.284 Water bridges: B:D.250, B:D.250

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

NAG.9: 2 residues within 4Å: Chain A: N.5, K.154 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.5, A:K.154 NAG.19: 3 residues within 4Å: Chain C: N.5, T.7, K.154 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.5, C:K.154, C:K.154 NAG.24: 4 residues within 4Å: Chain D: T.2, F.3, N.5, K.154 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:T.2, D:F.3, D:N.5 Water bridges: D:F.3, D:N.5

4 x G39: (3R,4R,5S)-4-(acetylamino)-5-amino-3-(pentan-3-yloxy)cyclohex-1-ene-1-carboxylic acid(Non-covalent)

G39.10: 13 residues within 4Å: Chain A: R.37, E.38, D.70, R.71, W.98, R.144, A.166, E.196, E.197, R.212, N.214, R.291, Y.325 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.98, A:A.166 Hydrogen bonds: A:E.38, A:D.70, A:R.71, A:Y.325 Water bridges: A:R.75, A:R.75, A:R.291 Salt bridges: A:R.37, A:R.212, A:R.291 G39.13: 14 residues within 4Å: Chain B: R.37, E.38, D.70, R.71, W.98, I.142, R.144, A.166, E.196, E.197, R.212, N.214, R.291, Y.325 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:W.98, B:A.166 Hydrogen bonds: B:E.38, B:R.71 Water bridges: B:D.70, B:D.70, B:R.71, B:R.75, B:E.147, B:R.291 Salt bridges: B:R.37, B:R.212, B:R.291 G39.20: 14 residues within 4Å: Chain C: R.37, E.38, D.70, R.71, W.98, I.142, R.144, A.166, E.196, E.197, R.212, N.214, R.291, Y.325 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:W.98, C:I.142, C:I.142, C:A.166 Hydrogen bonds: C:E.38, C:R.71, C:Y.325 Water bridges: C:R.75, C:E.147, C:R.291 Salt bridges: C:R.37, C:R.212, C:R.291 G39.25: 14 residues within 4Å: Chain D: R.37, E.38, D.70, R.71, W.98, I.142, R.144, A.166, E.196, E.197, R.212, N.214, R.291, Y.325 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:W.98, D:I.142, D:A.166, D:E.196 Hydrogen bonds: D:E.38, D:R.71 Water bridges: D:R.71, D:R.75, D:R.291 Salt bridges: D:R.37, D:R.212, D:R.291

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 7 residues within 4Å: Chain A: R.26 Chain B: H.63, N.65, G.66, T.67, H.69, S.72 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.55, B:N.65, B:S.72, A:R.26, A:R.26 GOL.14: 7 residues within 4Å: Chain B: R.26 Chain D: H.63, N.65, G.66, T.67, H.69, S.72 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:Q.55, D:N.65, D:H.69, D:S.72, B:R.26, B:R.26 Water bridges: D:Q.55 GOL.15: 2 residues within 4Å: Chain B: I.311 Ligands: GOL.16 No protein-ligand interaction detected (PLIP) GOL.16: 2 residues within 4Å: Chain B: I.311 Ligands: GOL.15 No protein-ligand interaction detected (PLIP) GOL.17: 4 residues within 4Å: Chain B: S.308, G.309, P.310, I.311 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.309 Water bridges: B:K.240, B:K.240 GOL.21: 8 residues within 4Å: Chain A: Q.55, H.63, N.65, G.66, T.67, H.69, S.72 Chain C: R.26 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:H.63, A:N.65, A:H.69, A:S.72, C:R.26, C:R.26 GOL.22: 8 residues within 4Å: Chain C: Q.55, H.63, N.65, G.66, T.67, H.69, S.72 Chain D: R.26 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:R.26, D:R.26, C:H.63, C:N.65, C:S.72 GOL.26: 7 residues within 4Å: Chain D: R.169, A.170, L.188, A.189, G.190, A.192, Q.193 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.169, D:A.170, D:L.188 Water bridges: D:G.190 GOL.27: 4 residues within 4Å: Chain D: V.206, T.224, I.225, D.226 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:I.225, D:D.226, D:D.226

4 x CA: CALCIUM ION(Non-covalent)

CA.12: 5 residues within 4Å: Chain A: D.213, G.217, D.244, P.267, G.268 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.213, A:G.217, A:D.244, A:P.267, H2O.3, H2O.12 CA.18: 5 residues within 4Å: Chain B: D.213, G.217, D.244, P.267, G.268 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.213, B:G.217, B:D.244, B:P.267, H2O.21, H2O.27 CA.23: 5 residues within 4Å: Chain C: D.213, G.217, D.244, P.267, G.268 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.213, C:G.217, C:D.244, C:P.267, H2O.38, H2O.48 CA.28: 5 residues within 4Å: Chain D: D.213, G.217, D.244, P.267, G.268 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.213, D:G.217, D:D.244, D:P.267, H2O.60, H2O.60

1 x CO2: CARBON DIOXIDE(Covalent)

CO2.29: 4 residues within 4Å: Chain D: K.8, N.335, K.336, E.337 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.8, D:N.335

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Salinger, M.T. et al., High Resolution Structures of Viral Neuraminidase with Drugs Bound in the Active Site. To Be Published

Release Date

2018-08-29

Peptides

Neuraminidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Neuraminidase

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