SMTL ID : 7u4f.1

Neuraminidase from influenza virus A/Moscow/10/1999(H3N2)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-tetramer

Ligands

4 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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: 9 residues within 4Å: Chain A: N.124 Chain C: D.254, Q.315, I.316, N.317, R.318, Y.377, G.378, T.379 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Q.315, C:I.316, C:N.317, C:R.318, C:N.317, C:N.317, C:R.318 Water bridges: C:Q.315, C:N.317, C:Y.377 NAG-NAG-BMA-MAN-MAN-MAN-MAN.7: 9 residues within 4Å: Chain B: N.124 Chain D: D.254, Q.315, I.316, N.317, R.318, Y.377, G.378, T.379 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Q.315, D:I.316, D:N.317, D:R.318, D:N.317, D:N.317, D:R.318 Water bridges: D:Q.315, D:N.317, D:Y.377 NAG-NAG-BMA-MAN-MAN-MAN-MAN.13: 9 residues within 4Å: Chain B: D.254, Q.315, I.316, N.317, R.318, Y.377, G.378, T.379 Chain C: N.124 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.315, B:I.316, B:N.317, B:R.318, B:N.317, B:N.317, B:R.318 Water bridges: B:Q.315, B:N.317, B:Y.377 NAG-NAG-BMA-MAN-MAN-MAN-MAN.19: 9 residues within 4Å: Chain A: D.254, Q.315, I.316, N.317, R.318, Y.377, G.378, T.379 Chain D: N.124 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.315, A:I.316, A:N.317, A:R.318, A:N.317, A:N.317, A:R.318 Water bridges: A:Q.315, A:N.317, A:Y.377

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

NAG-BMA.2: 2 residues within 4Å: Chain A: N.70, D.71 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.71 NAG-BMA.8: 2 residues within 4Å: Chain B: N.70, D.71 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.71 NAG-BMA.14: 2 residues within 4Å: Chain C: N.70, D.71 1 PLIP interactions: 1 interactions with chain C Water bridges: C:D.71 NAG-BMA.20: 2 residues within 4Å: Chain D: N.70, D.71 1 PLIP interactions: 1 interactions with chain D Water bridges: D:D.71

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 6 residues within 4Å: Chain A: D.217, G.221, D.248, G.269, H.271, G.272 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.217, A:G.221, A:D.248, A:G.269, A:H.271, H2O.6 CA.9: 6 residues within 4Å: Chain B: D.217, G.221, D.248, G.269, H.271, G.272 6 PLIP interactions: 5 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.217, B:G.221, B:D.248, B:G.269, B:H.271, H2O.29 CA.15: 6 residues within 4Å: Chain C: D.217, G.221, D.248, G.269, H.271, G.272 6 PLIP interactions: 5 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.217, C:G.221, C:D.248, C:G.269, C:H.271, H2O.51 CA.21: 6 residues within 4Å: Chain D: D.217, G.221, D.248, G.269, H.271, G.272 6 PLIP interactions: 5 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.217, D:G.221, D:D.248, D:G.269, D:H.271, H2O.73

12 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 5 residues within 4Å: Chain A: R.42, D.75, R.216, R.295, Y.330 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:D.75, A:Y.330 Water bridges: A:R.42, A:R.42, A:R.42, A:D.75, A:R.216, A:R.216 Salt bridges: A:R.42, A:R.216, A:R.295 SO4.5: 4 residues within 4Å: Chain A: S.258, S.259, H.260, N.265 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.258, A:S.258 Water bridges: A:H.260, A:H.260, A:E.267, A:E.267 Salt bridges: A:H.260 SO4.6: 2 residues within 4Å: Chain A: H.74, D.75 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.75 Water bridges: A:R.76, A:R.76, A:R.76, A:R.76 Salt bridges: A:H.74 SO4.10: 5 residues within 4Å: Chain B: R.42, D.75, R.216, R.295, Y.330 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:D.75, B:Y.330 Water bridges: B:R.42, B:R.42, B:R.42, B:D.75, B:R.216, B:R.216 Salt bridges: B:R.42, B:R.216, B:R.295 SO4.11: 4 residues within 4Å: Chain B: S.258, S.259, H.260, N.265 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.258, B:S.258 Water bridges: B:H.260, B:H.260, B:E.267, B:E.267 Salt bridges: B:H.260 SO4.12: 2 residues within 4Å: Chain B: H.74, D.75 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.75 Water bridges: B:R.76, B:R.76, B:R.76, B:R.76 Salt bridges: B:H.74 SO4.16: 5 residues within 4Å: Chain C: R.42, D.75, R.216, R.295, Y.330 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:D.75, C:Y.330 Water bridges: C:R.42, C:R.42, C:R.42, C:D.75, C:R.216, C:R.216 Salt bridges: C:R.42, C:R.216, C:R.295 SO4.17: 4 residues within 4Å: Chain C: S.258, S.259, H.260, N.265 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:S.258, C:S.258 Water bridges: C:H.260, C:H.260, C:E.267, C:E.267 Salt bridges: C:H.260 SO4.18: 2 residues within 4Å: Chain C: H.74, D.75 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:D.75 Water bridges: C:R.76, C:R.76, C:R.76, C:R.76 Salt bridges: C:H.74 SO4.22: 5 residues within 4Å: Chain D: R.42, D.75, R.216, R.295, Y.330 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:D.75, D:Y.330 Water bridges: D:R.42, D:R.42, D:R.42, D:D.75, D:R.216, D:R.216 Salt bridges: D:R.42, D:R.216, D:R.295 SO4.23: 4 residues within 4Å: Chain D: S.258, S.259, H.260, N.265 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:S.258, D:S.258 Water bridges: D:H.260, D:H.260, D:E.267, D:E.267 Salt bridges: D:H.260 SO4.24: 2 residues within 4Å: Chain D: H.74, D.75 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:D.75 Water bridges: D:R.76, D:R.76, D:R.76, D:R.76 Salt bridges: D:H.74

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lei, R. et al., Prevalence and mechanisms of evolutionary contingency in human influenza H3N2 neuraminidase. Nat Commun (2022)

Release Date

2022-10-19

Peptides

Neuraminidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Neuraminidase

Related Entries With Identical Sequence