SMTL ID : 2cml.1

Structure of Neuraminidase from English Duck Subtype N6 Complexed with 30 MM ZANAMIVIR, Crystal Soaked for 3 Hours at 291 K.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-tetramer

Ligands

3 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG-NAG.1: 3 residues within 4Å: Chain A: N.5, T.7, K.154 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 9 residues within 4Å: Chain C: N.120 Chain D: N.14, S.15, S.312, N.313, L.374, G.375, S.376 Ligands: BMA.31 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.313, D:N.313, D:N.313, D:N.313 NAG-NAG.5: 10 residues within 4Å: Chain B: N.14, S.15, S.312, N.313, R.373, L.374, G.375, S.376 Chain D: N.120 Ligands: BMA.39 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.313, B:N.313

1 x MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose

MAN-MAN-MAN.2: 9 residues within 4Å: Chain A: D.250, R.284, I.286, E.295, L.297, P.310, N.313, V.315 Ligands: BMA.11 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.250, A:R.284 Water bridges: A:E.295

1 x NAG- NAG- BMA- MAN- MAN: 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.3: 17 residues within 4Å: Chain A: N.119, N.120 Chain C: N.14, E.295, L.297, P.310, I.311, S.312, N.313, Q.314, V.315, R.373, L.374, G.375, S.376 Ligands: MAN.25, MAN.29 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.312, C:N.313, C:N.313, C:N.313, C:N.313 Water bridges: C:N.313, C:N.313

8 x ZMR: ZANAMIVIR(Non-covalent)

ZMR.6: 17 residues within 4Å: Chain A: R.37, E.38, L.53, D.70, R.71, R.75, W.98, I.142, R.144, E.147, A.166, E.196, E.197, R.212, N.214, R.291, Y.325 22 PLIP interactions: 22 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.325 Water bridges: A:R.75, A:R.75, A:S.99, A:E.197, A:E.197 Salt bridges: A:R.37, A:E.38, A:D.70, A:E.147, A:R.212, A:R.291 ZMR.7: 8 residues within 4Å: Chain A: S.287, D.289, S.290, S.292, N.319, Q.320, N.321, W.322 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.322 Hydrogen bonds: A:S.287, A:D.289, A:S.290, A:S.292, A:S.292, A:N.319, A:N.319 Water bridges: A:K.288 ZMR.12: 17 residues within 4Å: Chain B: R.37, E.38, L.53, D.70, R.71, R.75, W.98, I.142, R.144, E.147, 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:R.71, B:W.98, B:W.98, B:E.197, B:R.212, B:R.212 Water bridges: B:R.75 Salt bridges: B:R.37, B:E.38, B:D.70, B:E.147, B:R.212, B:R.291 ZMR.13: 9 residues within 4Å: Chain B: S.287, D.289, S.290, S.292, N.319, Q.320, N.321, W.322, K.353 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:W.322 Hydrogen bonds: B:S.287, B:D.289, B:S.290, B:S.292, B:S.292, B:N.319, B:Q.320 ZMR.22: 17 residues within 4Å: Chain C: R.37, E.38, L.53, D.70, R.71, R.75, W.98, I.142, R.144, E.147, 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:D.70, C:R.71, C:W.98, C:R.144, C:E.197, C:R.212, C:R.212, C:Y.325 Water bridges: C:E.147 Salt bridges: C:R.37, C:E.38, C:D.70, C:E.147, C:R.212, C:R.291 ZMR.23: 9 residues within 4Å: Chain C: S.287, D.289, S.290, S.292, N.319, Q.320, N.321, W.322, K.353 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:W.322 Hydrogen bonds: C:S.290, C:S.292, C:S.292, C:N.319, C:N.319 ZMR.32: 17 residues within 4Å: Chain D: R.37, E.38, L.53, D.70, R.71, R.75, W.98, I.142, R.144, E.147, 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:R.71, D:W.98, D:W.98, D:R.144, D:E.197, D:R.212 Water bridges: D:R.37 Salt bridges: D:R.37, D:E.38, D:D.70, D:E.147, D:R.212, D:R.291 ZMR.33: 9 residues within 4Å: Chain D: S.287, D.289, S.290, S.292, N.319, Q.320, N.321, W.322, K.353 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:W.322 Hydrogen bonds: D:S.287, D:S.290, D:S.292, D:S.292, D:N.319, D:N.319

4 x CA: CALCIUM ION(Non-covalent)

CA.8: 4 residues within 4Å: Chain A: D.213, G.217, D.244, P.267 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.213, A:G.217, A:D.244, A:P.267, H2O.3 CA.14: 4 residues within 4Å: Chain B: D.213, G.217, D.244, P.267 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.213, B:G.217, B:D.244, B:P.267, H2O.7 CA.24: 5 residues within 4Å: Chain C: D.213, G.217, D.244, P.267, G.268 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.213, C:G.217, C:D.244, C:P.267, H2O.11 CA.34: 4 residues within 4Å: Chain D: D.213, G.217, D.244, P.267 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.213, D:G.217, D:D.244, D:P.267, H2O.15

11 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-functional Binders)(Non-covalent)

NAG.9: 4 residues within 4Å: Chain A: N.65, L.358 Chain C: Y.387 Ligands: NAG.10 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.358 Hydrogen bonds: A:N.65 NAG.10: 1 residues within 4Å: Ligands: NAG.9 No protein-ligand interaction detected (PLIP) NAG.15: 4 residues within 4Å: Chain A: Y.387 Chain B: N.65, L.358 Ligands: NAG.16 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.358 Hydrogen bonds: B:N.65 NAG.16: 1 residues within 4Å: Ligands: NAG.15 No protein-ligand interaction detected (PLIP) NAG.17: 5 residues within 4Å: Chain A: R.373, L.374, G.375 Chain B: N.120 Ligands: NAG.18 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.120 NAG.18: 7 residues within 4Å: Chain A: N.14, S.15, S.312, N.313, Q.314 Ligands: BMA.11, NAG.17 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.313, A:N.313, A:N.313 NAG.26: 4 residues within 4Å: Chain C: T.2, F.3, N.5, K.154 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.2, C:F.3, C:N.5 NAG.27: 4 residues within 4Å: Chain C: N.65, L.358 Chain D: Y.387 Ligands: NAG.28 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:L.358 Hydrogen bonds: C:N.65, D:Y.387 NAG.28: 1 residues within 4Å: Ligands: NAG.27 No protein-ligand interaction detected (PLIP) NAG.37: 3 residues within 4Å: Chain D: N.5, T.7, K.154 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.5 NAG.38: 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

3 x BMA: beta-D-mannopyranose(Non-covalent)

BMA.11: 6 residues within 4Å: Chain A: P.310, I.311, S.312, N.313 Ligands: MAN-MAN-MAN.2, NAG.18 No protein-ligand interaction detected (PLIP) BMA.31: 6 residues within 4Å: Chain D: P.310, I.311, S.312, N.313 Ligands: NAG-NAG.4, MAN.35 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.313 BMA.39: 6 residues within 4Å: Chain B: P.310, I.311, S.312, N.313 Ligands: NAG-NAG.5, MAN.19 No protein-ligand interaction detected (PLIP)

8 x MAN: alpha-D-mannopyranose(Non-covalent)(Non-functional Binders)

MAN.19: 7 residues within 4Å: Chain B: E.295, L.297, P.310, N.313 Ligands: MAN.20, MAN.21, BMA.39 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.295 MAN.20: 3 residues within 4Å: Chain B: D.250, R.284 Ligands: MAN.19 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.250, B:D.250, B:R.284, B:R.284 MAN.21: 5 residues within 4Å: Chain B: I.286, E.295, N.313, V.315 Ligands: MAN.19 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.295, B:N.313 MAN.25: 3 residues within 4Å: Chain C: D.250, R.284 Ligands: NAG-NAG-BMA-MAN-MAN.3 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.250, C:R.284 MAN.29: 3 residues within 4Å: Ligands: NAG-NAG-BMA-MAN-MAN.3, NAG-NAG-BMA-MAN-MAN.3, MAN.30 No protein-ligand interaction detected (PLIP) MAN.30: 1 residues within 4Å: Ligands: MAN.29 No protein-ligand interaction detected (PLIP) MAN.35: 6 residues within 4Å: Chain D: E.295, L.297, P.310, N.313 Ligands: BMA.31, MAN.36 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.295 MAN.36: 6 residues within 4Å: Chain D: I.286, E.295, N.313, V.315, N.319 Ligands: MAN.35 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.313, D:N.319

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rudino-Pinera, E. et al., The Crystal Structure of Type a Influenza Virus Neuraminidase of the N6 Subtype Reveals the Existence of Two Separate Neu5Ac Binding Sites. To be Published

Release Date

2007-06-05

Peptides

NEURAMINIDASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

NEURAMINIDASE

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