SMTL ID : 6hfy.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-tetramer

Ligands

2 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: 3 residues within 4Å: Chain A: Y.387 Chain B: N.65, L.358 No protein-ligand interaction detected (PLIP)

1 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

3 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.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 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.313, A:N.313, A:N.313, A:N.313, A:R.373, A:N.313, A:D.250, A:R.284, A:R.284 Water bridges: A:D.250, A:D.250 NAG-NAG-BMA-MAN-MAN-MAN.5: 16 residues within 4Å: Chain C: N.120 Chain D: N.14, 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 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.313, D:N.313, D:N.313, D:N.313, D:R.373, D:R.373, D:N.313, D:N.313, D:R.284, D:R.284 Water bridges: D:D.250, D:E.295 NAG-NAG-BMA-MAN-MAN-MAN.6: 16 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, 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:D.250, B:R.284, B:R.284 Water bridges: B:D.250, B:D.250

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

NAG.7: 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.12: 2 residues within 4Å: Chain B: N.5, K.154 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.5, B:K.154 NAG.19: 3 residues within 4Å: Chain C: N.65, L.358 Chain D: Y.387 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.358 Hydrogen bonds: C:N.65 NAG.20: 2 residues within 4Å: Chain C: N.5, K.154 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.5, C:K.154 NAG.25: 3 residues within 4Å: Chain B: Y.387 Chain D: N.65, L.358 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:L.358 Hydrogen bonds: D:N.65

4 x DAN: 2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID(Non-covalent)

DAN.8: 14 residues within 4Å: Chain A: 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 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:W.98, A:I.142, A:R.144 Hydrogen bonds: A:E.38, A:R.71, A:R.144, A:E.197, A:R.212, A:R.212, A:Y.325 Water bridges: A:R.37, A:E.147, A:E.197, A:E.197, A:R.291 Salt bridges: A:R.37, A:R.212, A:R.291 DAN.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 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:W.98, B:I.142, B:R.144 Hydrogen bonds: B:E.38, B:R.71, B:R.144, B:E.197, B:R.212, B:R.212 Water bridges: B:R.37, B:D.70, B:E.147, B:E.197 Salt bridges: B:R.37, B:R.212, B:R.291 DAN.21: 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 18 PLIP interactions: 18 interactions with chain C Hydrophobic interactions: C:W.98, C:I.142, C:R.144 Hydrogen bonds: C:E.38, C:R.71, C:R.144, C:E.197, C:R.212, C:R.212, C:Y.325 Water bridges: C:R.37, C:E.147, C:E.197, C:E.197, C:R.291 Salt bridges: C:R.37, C:R.212, C:R.291 DAN.26: 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 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:W.98, D:I.142, D:R.144 Hydrogen bonds: D:E.38, D:R.71, D:R.144, D:E.197, D:R.212, D:R.212 Water bridges: D:R.37, D:E.147, D:E.197, D:R.291 Salt bridges: D:R.37, D:R.212, D:R.291

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 6 residues within 4Å: Chain A: R.26 Chain B: H.63, N.65, G.66, T.67, S.72 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.55, B:H.63, B:S.72, A:R.26, A:R.26 Water bridges: B:Q.55 GOL.10: 6 residues within 4Å: Chain A: E.29, D.30, A.31, H.32, R.60 Chain C: D.30 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.30, A:A.31 Water bridges: A:R.60 GOL.14: 7 residues within 4Å: Chain B: R.26 Chain D: Q.55, H.63, N.65, G.66, T.67, S.72 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain D Hydrogen bonds: B:R.26, B:R.26, D:Q.55, D:N.65, D:S.72 GOL.15: 6 residues within 4Å: Chain B: R.1, P.45, Q.46, H.104, G.106, M.107 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.1, B:R.1, B:H.104 Water bridges: B:R.109 GOL.16: 7 residues within 4Å: Chain B: R.169, A.170, L.188, A.189, G.190, A.192, Q.193 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.169, B:A.170, B:G.190 Water bridges: B:G.190, B:G.190 GOL.22: 6 residues within 4Å: Chain A: Q.55, H.63, N.65, T.67, S.72 Chain C: R.26 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:Q.55, C:R.26, C:R.26 Water bridges: A:H.63, A:N.65, A:S.72 GOL.23: 6 residues within 4Å: Chain C: A.170, L.188, A.189, G.190, A.192, Q.193 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:A.170, C:L.188 Water bridges: C:R.169, C:R.169 GOL.27: 7 residues within 4Å: Chain C: Q.55, H.63, N.65, G.66, T.67, S.72 Chain D: R.26 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:Q.55, C:S.72, D:R.26, D:R.26 Water bridges: C:H.63, C:N.65 GOL.28: 2 residues within 4Å: Chain D: V.206, D.226 1 PLIP interactions: 1 interactions with chain D Water bridges: D:D.226

5 x CA: CALCIUM ION(Non-covalent)

CA.11: 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.2, H2O.10 CA.17: 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.18, H2O.22 CA.18: 4 residues within 4Å: Chain A: H.32 Chain B: H.32 Chain C: H.32 Chain D: H.32 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Metal complexes: D:H.32, B:H.32 CA.24: 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.30, H2O.34 CA.29: 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.42, H2O.44

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. (In preparation). 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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