SMTL ID : 1v0z.1

Structure of Neuraminidase from English duck subtype N6

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.84 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: 2 residues within 4Å: Chain A: N.5, K.154 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 9 residues within 4Å: Chain C: N.120 Chain D: N.14, S.312, N.313, R.373, L.374, G.375, S.376 Ligands: BMA-MAN.6 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:N.313, D:N.313, D:N.313, D:N.313, D:R.373, D:R.373

1 x 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

NAG-BMA-MAN-MAN.2: 13 residues within 4Å: Chain A: N.14, S.15, E.295, L.297, P.310, I.311, S.312, N.313, Q.314, R.373 Ligands: NAG.10, MAN.11, MAN.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.313, A:N.313, A:N.313, A:N.313

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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-MAN.3: 14 residues within 4Å: Chain A: N.119, N.120 Chain C: N.14, L.297, P.310, I.311, S.312, N.313, R.373, L.374, G.375, S.376 Ligands: MAN.14, MAN.15 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.313, C:N.313, C:N.313, C:N.313, C:N.313, C:N.313, C:E.295

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.4: 10 residues within 4Å: Chain B: N.14, E.295, L.297, P.310, I.311, S.312, N.313 Ligands: MAN.20, MAN.21, NAG.33 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.313, B:N.313, B:E.295

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

BMA-MAN.6: 8 residues within 4Å: Chain D: E.295, L.297, P.310, I.311, S.312, N.313 Ligands: NAG-NAG.5, MAN.34 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.313, D:N.313

4 x CA: CALCIUM ION(Non-covalent)

CA.7: 5 residues within 4Å: Chain A: D.213, G.217, D.244, P.267, G.268 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.5 CA.16: 4 residues within 4Å: Chain B: D.213, G.217, D.244, P.267 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.23, H2O.24 CA.23: 4 residues within 4Å: Chain C: D.213, G.217, D.244, P.267 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.38 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.55, H2O.57

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 6 residues within 4Å: Chain A: Q.55, H.63, N.65, 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.17: 8 residues within 4Å: Chain A: R.26 Chain B: Q.55, H.63, N.65, T.67, S.72, F.74, R.75 7 PLIP interactions: 5 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 Water bridges: B:H.69 GOL.25: 7 residues within 4Å: Chain C: Q.55, H.63, N.65, S.72, F.74, R.75 Chain D: R.26 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:Q.55, C:N.65, C:S.72, D:R.26, D:R.26 Water bridges: C:Q.55 GOL.30: 7 residues within 4Å: Chain B: R.26 Chain D: Q.55, H.63, N.65, S.72, F.74, R.75 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain D Hydrogen bonds: B:R.26, B:R.26, D:Q.55, D:N.65, D:S.72 Water bridges: D:Q.55

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

NAG.9: 4 residues within 4Å: Chain A: N.65, L.358 Chain C: Y.387 Ligands: NAG.22 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.358 Hydrogen bonds: A:N.65 NAG.10: 6 residues within 4Å: Chain A: R.373, L.374, G.375 Chain B: N.119, N.120 Ligands: NAG-BMA-MAN-MAN.2 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:L.374, B:N.119, B:N.120 NAG.13: 1 residues within 4Å: Ligands: NAG.19 No protein-ligand interaction detected (PLIP) NAG.18: 3 residues within 4Å: Chain B: T.2, N.5, K.154 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.5 Water bridges: B:R.1 NAG.19: 4 residues within 4Å: Chain A: Y.387 Chain B: N.65, L.358 Ligands: NAG.13 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.358 Hydrogen bonds: B:N.65 NAG.22: 1 residues within 4Å: Ligands: NAG.9 No protein-ligand interaction detected (PLIP) NAG.26: 3 residues within 4Å: Chain C: T.2, F.3, N.5 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.2, C:T.2, C:N.5 NAG.27: 4 residues within 4Å: Chain C: N.65, L.358 Chain D: Y.387 Ligands: NAG.28 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.358 Hydrogen bonds: C:N.65 NAG.28: 2 residues within 4Å: Chain D: I.386 Ligands: NAG.27 No protein-ligand interaction detected (PLIP) NAG.31: 4 residues within 4Å: Chain D: F.3, N.5, T.7, K.154 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:T.7 Hydrogen bonds: D:N.5 Water bridges: D:F.3 NAG.32: 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 NAG.33: 5 residues within 4Å: Chain B: L.374, G.375, S.376 Chain D: N.120 Ligands: NAG-BMA-MAN.4 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain D Hydrogen bonds: B:S.376 Water bridges: B:S.376, D:N.119, D:N.119, D:N.120, D:N.120, D:N.120

7 x MAN: alpha-D-mannopyranose(Non-covalent)

MAN.11: 4 residues within 4Å: Chain A: D.250, R.284, P.310 Ligands: NAG-BMA-MAN-MAN.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.250, A:R.284, A:R.284 Water bridges: A:D.250, A:R.284, A:K.288 MAN.12: 5 residues within 4Å: Chain A: E.295, L.297, N.313, V.315 Ligands: NAG-BMA-MAN-MAN.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.295, A:N.313 MAN.14: 4 residues within 4Å: Chain C: D.250, R.284, P.310 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.3 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.284 Water bridges: C:D.250, C:E.295 MAN.15: 5 residues within 4Å: Chain C: E.295, L.297, N.313, V.315 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.3 1 PLIP interactions: 1 interactions with chain C Water bridges: C:N.313 MAN.20: 3 residues within 4Å: Chain B: D.250, R.284 Ligands: NAG-BMA-MAN.4 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.250, B:D.250, B:R.284, B:R.284 Water bridges: B:D.250, B:D.250 MAN.21: 4 residues within 4Å: Chain B: E.295, N.313, V.315 Ligands: NAG-BMA-MAN.4 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.295, B:N.313 MAN.34: 4 residues within 4Å: Chain D: I.286, E.295, V.315 Ligands: BMA-MAN.6 4 PLIP interactions: 4 interactions with chain D Water bridges: D:R.284, D:N.313, D:N.319, D:Q.320

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

PEG.24: 10 residues within 4Å: Chain A: P.131, I.132, E.134 Chain C: H.17, D.331, K.336, N.340, C.342, C.368, G.369 6 PLIP interactions: 5 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, C:K.371

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rudino-Pinera, E. et al., The Crystal Structure of Influenza Type a Virus Neuraminidase of the N6 Subtype at 1.85 A Resolution. 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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