SMTL ID : 6mcx.1

INFLUENZA VIRUS NEURAMINIDASE SUBTYPE N9 (TERN) RECOMBINANT HEAD DOMAIN

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

4 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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-MAN.1: 20 residues within 4Å: Chain A: N.119, N.120, R.140 Chain C: R.247, N.249, D.250, R.283, I.285, I.287, E.294, L.296, K.308, P.309, T.310, Q.311, G.312, F.372, L.373, G.374, Q.375 8 PLIP interactions: 8 interactions with chain C Water bridges: C:T.310, C:Q.311, C:Q.311, C:T.314, C:Q.375, C:Q.375 Hydrophobic interactions: C:F.372 Hydrogen bonds: C:G.312, C:G.312 NAG-NAG-BMA-MAN-MAN-MAN-MAN.8: 20 residues within 4Å: Chain B: N.119, N.120, R.140 Chain D: R.247, N.249, D.250, R.283, I.285, I.287, E.294, L.296, K.308, P.309, T.310, Q.311, G.312, F.372, L.373, G.374, Q.375 8 PLIP interactions: 8 interactions with chain D Water bridges: D:T.310, D:Q.311, D:Q.311, D:T.314, D:Q.375, D:Q.375 Hydrophobic interactions: D:F.372 Hydrogen bonds: D:G.312, D:G.312 NAG-NAG-BMA-MAN-MAN-MAN-MAN.15: 20 residues within 4Å: Chain B: R.247, N.249, D.250, R.283, I.285, I.287, E.294, L.296, K.308, P.309, T.310, Q.311, G.312, F.372, L.373, G.374, Q.375 Chain C: N.119, N.120, R.140 8 PLIP interactions: 8 interactions with chain B Water bridges: B:T.310, B:Q.311, B:Q.311, B:T.314, B:Q.375, B:Q.375 Hydrophobic interactions: B:F.372 Hydrogen bonds: B:G.312, B:G.312 NAG-NAG-BMA-MAN-MAN-MAN-MAN.22: 20 residues within 4Å: Chain A: R.247, N.249, D.250, R.283, I.285, I.287, E.294, L.296, K.308, P.309, T.310, Q.311, G.312, F.372, L.373, G.374, Q.375 Chain D: N.119, N.120, R.140 8 PLIP interactions: 8 interactions with chain A Water bridges: A:T.310, A:Q.311, A:Q.311, A:T.314, A:Q.375, A:Q.375 Hydrophobic interactions: A:F.372 Hydrogen bonds: A:G.312, A:G.312

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

NAG.2: 4 residues within 4Å: Chain A: D.2, F.3, N.5, N.154 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:D.2 Hydrogen bonds: A:D.2, A:F.3, A:N.5 Water bridges: A:F.3, A:N.5 NAG.3: 2 residues within 4Å: Chain A: N.65, W.357 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.65, A:W.357 NAG.9: 4 residues within 4Å: Chain B: D.2, F.3, N.5, N.154 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:D.2 Hydrogen bonds: B:D.2, B:F.3, B:N.5 Water bridges: B:F.3, B:N.5 NAG.10: 2 residues within 4Å: Chain B: N.65, W.357 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.65, B:W.357 NAG.16: 4 residues within 4Å: Chain C: D.2, F.3, N.5, N.154 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:D.2 Hydrogen bonds: C:D.2, C:F.3, C:N.5 Water bridges: C:F.3, C:N.5 NAG.17: 2 residues within 4Å: Chain C: N.65, W.357 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.65, C:W.357 NAG.23: 4 residues within 4Å: Chain D: D.2, F.3, N.5, N.154 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:D.2 Hydrogen bonds: D:D.2, D:F.3, D:N.5 Water bridges: D:F.3, D:N.5 NAG.24: 2 residues within 4Å: Chain D: N.65, W.357 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.65, D:W.357

4 x CA: CALCIUM ION(Non-covalent)

CA.4: 5 residues within 4Å: Chain A: D.213, G.217, D.244, N.266, G.267 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.213, A:G.217, A:D.244, H2O.1, H2O.7 CA.11: 5 residues within 4Å: Chain B: D.213, G.217, D.244, N.266, G.267 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.213, B:G.217, B:D.244, H2O.15, H2O.21 CA.18: 5 residues within 4Å: Chain C: D.213, G.217, D.244, N.266, G.267 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.213, C:G.217, C:D.244, H2O.29, H2O.35 CA.25: 5 residues within 4Å: Chain D: D.213, G.217, D.244, N.266, G.267 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.213, D:G.217, D:D.244, H2O.43, H2O.49

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain C: C.11, A.333, E.334, G.335, E.336, C.337, R.339 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:E.336, C:R.339 Water bridges: C:R.339, C:R.339, C:R.339, A:K.181 GOL.6: 6 residues within 4Å: Chain A: R.37, D.70, R.212, G.267, R.290, Y.324 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.37, A:R.37, A:R.212, A:R.212, A:G.267, A:R.290, A:R.290 GOL.7: 3 residues within 4Å: Chain A: I.68, H.69, D.70 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.70, A:D.70, A:D.70 Water bridges: A:I.68, A:D.70 GOL.12: 7 residues within 4Å: Chain D: C.11, A.333, E.334, G.335, E.336, C.337, R.339 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:E.336, D:R.339 Water bridges: D:R.339, D:R.339, D:R.339, B:K.181 GOL.13: 6 residues within 4Å: Chain B: R.37, D.70, R.212, G.267, R.290, Y.324 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.37, B:R.37, B:R.212, B:R.212, B:G.267, B:R.290, B:R.290 GOL.14: 3 residues within 4Å: Chain B: I.68, H.69, D.70 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.70, B:D.70, B:D.70 Water bridges: B:I.68, B:D.70 GOL.19: 7 residues within 4Å: Chain B: C.11, A.333, E.334, G.335, E.336, C.337, R.339 6 PLIP interactions: 1 interactions with chain C, 5 interactions with chain B Water bridges: C:K.181, B:R.339, B:R.339, B:R.339 Hydrogen bonds: B:E.336, B:R.339 GOL.20: 6 residues within 4Å: Chain C: R.37, D.70, R.212, G.267, R.290, Y.324 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:R.37, C:R.37, C:R.212, C:R.212, C:G.267, C:R.290, C:R.290 GOL.21: 3 residues within 4Å: Chain C: I.68, H.69, D.70 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:D.70, C:D.70, C:D.70 Water bridges: C:I.68, C:D.70 GOL.26: 7 residues within 4Å: Chain A: C.11, A.333, E.334, G.335, E.336, C.337, R.339 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:E.336, A:R.339 Water bridges: A:R.339, A:R.339, A:R.339, D:K.181 GOL.27: 6 residues within 4Å: Chain D: R.37, D.70, R.212, G.267, R.290, Y.324 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:R.37, D:R.37, D:R.212, D:R.212, D:G.267, D:R.290, D:R.290 GOL.28: 3 residues within 4Å: Chain D: I.68, H.69, D.70 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:D.70, D:D.70, D:D.70 Water bridges: D:I.68, D:D.70

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Streltsov, V.A. et al., Structure of an Influenza A virus N9 neuraminidase with a tetrabrachion-domain stalk. Acta Crystallogr.,Sect.F (2019)

Release Date

2019-01-23

Peptides

Neuraminidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Neuraminidase

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