SMTL ID : 6d3b.1

INFLUENZA VIRUS NEURAMINIDASE SUBTYPE N9 (TERN) APO FORM

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-tetramer

Ligands

4 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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-MAN-MAN-MAN.1: 19 residues within 4Å: Chain A: N.120, N.121 Chain C: R.248, N.250, D.251, R.284, I.286, I.288, E.295, L.297, K.309, P.310, T.311, Q.312, G.313, F.373, L.374, G.375, Q.376 5 PLIP interactions: 5 interactions with chain C Water bridges: C:G.313, C:Q.312, C:Q.312, C:Q.376 Hydrophobic interactions: C:F.373 Hydrogen bonds: C:G.313 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.10: 19 residues within 4Å: Chain B: N.120, N.121 Chain D: R.248, N.250, D.251, R.284, I.286, I.288, E.295, L.297, K.309, P.310, T.311, Q.312, G.313, F.373, L.374, G.375, Q.376 5 PLIP interactions: 5 interactions with chain D Water bridges: D:G.313, D:Q.312, D:Q.312, D:Q.376 Hydrophobic interactions: D:F.373 Hydrogen bonds: D:G.313 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.19: 19 residues within 4Å: Chain B: R.248, N.250, D.251, R.284, I.286, I.288, E.295, L.297, K.309, P.310, T.311, Q.312, G.313, F.373, L.374, G.375, Q.376 Chain C: N.120, N.121 5 PLIP interactions: 5 interactions with chain B Water bridges: B:G.313, B:Q.312, B:Q.312, B:Q.376 Hydrophobic interactions: B:F.373 Hydrogen bonds: B:G.313 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.28: 19 residues within 4Å: Chain A: R.248, N.250, D.251, R.284, I.286, I.288, E.295, L.297, K.309, P.310, T.311, Q.312, G.313, F.373, L.374, G.375, Q.376 Chain D: N.120, N.121 5 PLIP interactions: 5 interactions with chain A Water bridges: A:G.313, A:Q.312, A:Q.312, A:Q.376 Hydrophobic interactions: A:F.373 Hydrogen bonds: A:G.313

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

NAG-NAG.2: 4 residues within 4Å: Chain A: D.3, F.4, N.6, N.155 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.3 Water bridges: A:N.155, A:N.155 NAG-NAG.11: 4 residues within 4Å: Chain B: D.3, F.4, N.6, N.155 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.3 Water bridges: B:N.155, B:N.155 NAG-NAG.20: 4 residues within 4Å: Chain C: D.3, F.4, N.6, N.155 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.3 Water bridges: C:N.155, C:N.155 NAG-NAG.29: 4 residues within 4Å: Chain D: D.3, F.4, N.6, N.155 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.3 Water bridges: D:N.155, D:N.155

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

NAG.3: 2 residues within 4Å: Chain A: N.66, W.358 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.66, A:W.358 NAG.12: 2 residues within 4Å: Chain B: N.66, W.358 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.66, B:W.358 NAG.21: 2 residues within 4Å: Chain C: N.66, W.358 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.66, C:W.358 NAG.30: 2 residues within 4Å: Chain D: N.66, W.358 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.66, D:W.358

8 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.4: 5 residues within 4Å: Chain A: D.214, G.218, D.245, N.267, G.268 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.214, A:G.218, A:D.245, A:N.267, H2O.1, H2O.12 CA.5: 3 residues within 4Å: Ligands: CA.14, CA.23, CA.32 No protein-ligand interaction detected (PLIP) CA.13: 5 residues within 4Å: Chain B: D.214, G.218, D.245, N.267, G.268 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.214, B:G.218, B:D.245, B:N.267, H2O.29, H2O.40 CA.14: 3 residues within 4Å: Ligands: CA.5, CA.23, CA.32 No protein-ligand interaction detected (PLIP) CA.22: 5 residues within 4Å: Chain C: D.214, G.218, D.245, N.267, G.268 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.214, C:G.218, C:D.245, C:N.267, H2O.57, H2O.68 CA.23: 3 residues within 4Å: Ligands: CA.5, CA.14, CA.32 No protein-ligand interaction detected (PLIP) CA.31: 5 residues within 4Å: Chain D: D.214, G.218, D.245, N.267, G.268 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.214, D:G.218, D:D.245, D:N.267, H2O.85, H2O.95 CA.32: 3 residues within 4Å: Ligands: CA.5, CA.14, CA.23 No protein-ligand interaction detected (PLIP)

16 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 5 residues within 4Å: Chain C: C.12, A.334, E.335, C.338, R.340 Ligand excluded by PLIP GOL.7: 4 residues within 4Å: Chain A: S.287, A.289, S.290, N.319 Ligand excluded by PLIP GOL.8: 6 residues within 4Å: Chain A: H.64, N.66, G.67, T.68, Y.75 Chain C: R.27 Ligand excluded by PLIP GOL.9: 5 residues within 4Å: Chain A: L.189, A.190, G.191, A.193, K.194 Ligand excluded by PLIP GOL.15: 5 residues within 4Å: Chain D: C.12, A.334, E.335, C.338, R.340 Ligand excluded by PLIP GOL.16: 4 residues within 4Å: Chain B: S.287, A.289, S.290, N.319 Ligand excluded by PLIP GOL.17: 6 residues within 4Å: Chain B: H.64, N.66, G.67, T.68, Y.75 Chain D: R.27 Ligand excluded by PLIP GOL.18: 5 residues within 4Å: Chain B: L.189, A.190, G.191, A.193, K.194 Ligand excluded by PLIP GOL.24: 5 residues within 4Å: Chain B: C.12, A.334, E.335, C.338, R.340 Ligand excluded by PLIP GOL.25: 4 residues within 4Å: Chain C: S.287, A.289, S.290, N.319 Ligand excluded by PLIP GOL.26: 6 residues within 4Å: Chain B: R.27 Chain C: H.64, N.66, G.67, T.68, Y.75 Ligand excluded by PLIP GOL.27: 5 residues within 4Å: Chain C: L.189, A.190, G.191, A.193, K.194 Ligand excluded by PLIP GOL.33: 5 residues within 4Å: Chain A: C.12, A.334, E.335, C.338, R.340 Ligand excluded by PLIP GOL.34: 4 residues within 4Å: Chain D: S.287, A.289, S.290, N.319 Ligand excluded by PLIP GOL.35: 6 residues within 4Å: Chain A: R.27 Chain D: H.64, N.66, G.67, T.68, Y.75 Ligand excluded by PLIP GOL.36: 5 residues within 4Å: Chain D: L.189, A.190, G.191, A.193, K.194 Ligand excluded by PLIP

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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