SMTL ID : 1w1x.1

Structure of Neuraminidase from English duck subtype N6 complexed with 30 mM sialic acid (NANA, Neu5Ac), crystal soaked for 3 hours at 277 K.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

1 x BMA- MAN- MAN: alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose

BMA-MAN-MAN.1: 10 residues within 4Å: Chain A: D.250, R.284, E.295, L.297, P.310, I.311, S.312, N.313 Ligands: NAG-NAG.2, MAN.10 3 PLIP interactions: 3 interactions with chain A Water bridges: A:N.313, A:D.250 Hydrogen bonds: A:D.250, A:R.284

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

NAG-NAG.2: 10 residues within 4Å: Chain A: S.15, S.312, N.313, Q.314, R.373, L.374, G.375 Chain B: N.119, N.120 Ligands: BMA-MAN-MAN.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.312, A:N.313, A:N.313, A:R.373 NAG-NAG.6: 8 residues within 4Å: Chain C: N.120 Chain D: N.14, S.312, N.313, L.374, G.375, S.376 Ligands: BMA.32 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.313, D:N.313, D:N.313, D:N.313

1 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.3: 9 residues within 4Å: Chain B: P.310, I.311, S.312, N.313, L.374, G.375, S.376 Chain D: N.120 Ligands: MAN-MAN.4 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.313, B:N.313

1 x MAN- MAN: alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose(Non-covalent)

MAN-MAN.4: 8 residues within 4Å: Chain B: D.250, R.284, E.295, L.297, P.310, N.313 Ligands: NAG-NAG-BMA.3, MAN.17 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.250, B:D.250, B:R.284, B:R.284

1 x NAG- BMA- MAN: alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-BMA-MAN.5: 12 residues within 4Å: Chain C: N.14, S.15, L.297, P.310, I.311, S.312, N.313, Q.314, R.373 Ligands: MAN.24, MAN.25, MAN.26 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:N.313, C:N.313, C:E.295, C:N.313, C:N.313, C:N.313, C:N.313, C:R.373 Water bridges: C:R.284

8 x SIA: N-acetyl-alpha-neuraminic acid(Non-covalent)

SIA.7: 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 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:W.98 Hydrogen bonds: A:E.38, A:D.70, A:R.71, A:R.144, A:E.197, A:R.212, A:Y.325 Water bridges: A:R.37, A:R.37, A:R.37, A:E.147, A:E.147, A:E.147, A:E.197, A:E.197, A:R.212, A:R.291 Salt bridges: A:R.37, A:R.212, A:R.291 SIA.8: 8 residues within 4Å: Chain A: S.287, S.290, S.292, N.319, Q.320, N.321, W.322, K.353 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.322 Hydrogen bonds: A:S.287, A:S.290, A:S.292, A:S.292, A:N.319, A:N.319 Water bridges: A:D.289 SIA.14: 13 residues within 4Å: Chain B: 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 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:W.98 Hydrogen bonds: B:E.38, B:D.70, B:R.71, B:E.197, B:R.212 Water bridges: B:R.37, B:R.37, B:D.70, B:E.147, B:E.147, B:R.291 Salt bridges: B:R.37, B:R.212, B:R.291 SIA.15: 8 residues within 4Å: Chain B: S.287, S.290, S.292, N.319, Q.320, N.321, W.322, K.353 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:W.322 Hydrogen bonds: B:S.287, B:S.287, B:S.290, B:S.292, B:S.292, B:N.319, B:N.319, B:N.319 Water bridges: B:K.288, B:D.289 SIA.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 21 PLIP interactions: 21 interactions with chain C Hydrophobic interactions: C:W.98, C:I.142 Hydrogen bonds: C:E.38, C:D.70, C:D.70, C:D.70, C:R.71, C:R.144, C:E.197, C:R.212, C:R.212, C:Y.325 Water bridges: C:R.37, C:R.37, C:R.37, C:E.147, C:E.197, C:E.197 Salt bridges: C:R.37, C:R.212, C:R.291 SIA.22: 8 residues within 4Å: Chain C: S.287, S.290, S.292, N.319, Q.320, N.321, W.322, K.353 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:W.322 Hydrogen bonds: C:S.287, C:S.290, C:S.292, C:S.292, C:N.319, C:N.319, C:N.319 SIA.29: 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 19 PLIP interactions: 19 interactions with chain D Hydrophobic interactions: D:W.98, D:I.142 Hydrogen bonds: D:E.38, D:D.70, D:D.70, D:R.71, D:R.144, D:E.197, D:R.212, D:R.212 Water bridges: D:R.37, D:R.37, D:R.37, D:E.147, D:E.197, D:R.291 Salt bridges: D:R.37, D:R.212, D:R.291 SIA.30: 8 residues within 4Å: Chain D: S.287, S.290, S.292, N.319, Q.320, N.321, W.322, K.353 10 PLIP interactions: 10 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, D:N.319 Water bridges: D:Q.320, D:K.353

4 x CA: CALCIUM ION(Non-covalent)

CA.9: 4 residues within 4Å: Chain A: D.213, G.217, D.244, P.267 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.213, A:G.217, A:D.244, A:P.267 CA.16: 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.26 CA.23: 4 residues within 4Å: Chain C: D.213, G.217, D.244, P.267 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.213, C:G.217, C:D.244, C:P.267 CA.31: 5 residues within 4Å: Chain D: D.213, G.217, D.244, P.267, G.268 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.213, D:G.217, D:D.244, D:P.267

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

MAN.10: 5 residues within 4Å: Chain A: E.295, L.297, N.313, V.315 Ligands: BMA-MAN-MAN.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.295 Water bridges: A:N.313 MAN.17: 4 residues within 4Å: Chain B: E.295, N.313, V.315 Ligands: MAN-MAN.4 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.295, B:N.313 MAN.24: 2 residues within 4Å: Ligands: NAG-BMA-MAN.5, NAG-BMA-MAN.5 No protein-ligand interaction detected (PLIP) MAN.25: 3 residues within 4Å: Chain C: D.250, R.284 Ligands: NAG-BMA-MAN.5 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.250, C:R.284 Water bridges: C:D.250, C:D.250 MAN.26: 5 residues within 4Å: Chain C: E.295, L.297, N.313, V.315 Ligands: NAG-BMA-MAN.5 1 PLIP interactions: 1 interactions with chain C Water bridges: C:N.313

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

NAG.11: 2 residues within 4Å: Chain A: N.5, K.154 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.154 Water bridges: A:N.5 NAG.12: 3 residues within 4Å: Chain A: N.65, L.358 Chain C: Y.387 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.358 Hydrogen bonds: A:N.65 NAG.18: 3 residues within 4Å: Chain A: Y.387 Chain B: N.65, L.358 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.358 Hydrogen bonds: B:N.65 NAG.27: 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.33: 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 GOL: GLYCEROL(Non-functional Binders)

GOL.13: 7 residues within 4Å: Chain A: Q.55, H.63, N.65, H.69, S.72, F.74 Chain C: R.26 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:Q.55, A:N.65, A:S.72, C:R.26, C:R.26 Water bridges: A:Q.55 GOL.19: 6 residues within 4Å: Chain A: R.26 Chain B: Q.55, H.63, N.65, S.72, F.74 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.55, B:Q.55, B:N.65, B:S.72, A:R.26, A:R.26 GOL.28: 6 residues within 4Å: Chain C: Q.55, H.63, N.65, S.72, F.74 Chain D: R.26 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:R.26, D:R.26, C:Q.55, C:N.65, C:S.72 Water bridges: C:Q.55 GOL.34: 6 residues within 4Å: Chain B: R.26 Chain D: Q.55, H.63, N.65, S.72, F.74 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:Q.55, D:N.65, D:S.72, B:R.26, B:R.26 Water bridges: D:Q.55

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.20: 8 residues within 4Å: Chain A: P.131, E.134 Chain C: H.17, K.336, N.340, C.342, C.368, G.369 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:K.336, A:E.134 Water bridges: C:D.331, C:D.331, C:K.371

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

BMA.32: 4 residues within 4Å: Chain D: I.311, S.312, N.313 Ligands: NAG-NAG.6 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.313

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

2006-01-25

Peptides

NEURAMINIDASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

NEURAMINIDASE

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