SMTL ID : 8dwb.1

Neuraminidase from influenza virus A/Moscow/10/1999(H3N2) in complex with sialic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

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

NAG-NAG-BMA-MAN-MAN.1: 10 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 Ligands: MAN.4 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:I.316, C:N.317, C:R.318, C:N.317, C:N.317, C:R.318 Water bridges: C:Y.377, C:Y.377 NAG-NAG-BMA-MAN-MAN.8: 10 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 Ligands: MAN.11 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:I.316, D:N.317, D:R.318, D:N.317, D:N.317, D:R.318 Water bridges: D:Y.377, D:Y.377 NAG-NAG-BMA-MAN-MAN.15: 10 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 Ligands: MAN.18 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:I.316, B:N.317, B:R.318, B:N.317, B:N.317, B:R.318 Water bridges: B:Y.377, B:Y.377 NAG-NAG-BMA-MAN-MAN.22: 10 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 Ligands: MAN.25 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.316, A:N.317, A:R.318, A:N.317, A:N.317, A:R.318 Water bridges: A:Y.377, A:Y.377

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: 2 residues within 4Å: Chain A: N.70, D.71 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain B: N.70, D.71 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 2 residues within 4Å: Chain C: N.70, D.71 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 2 residues within 4Å: Chain D: N.70, D.71 No protein-ligand interaction detected (PLIP)

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

SIA.3: 13 residues within 4Å: Chain A: R.42, E.43, D.75, R.76, W.102, R.148, A.170, E.200, E.201, R.216, N.218, R.295, Y.330 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:D.75, A:R.76 Hydrogen bonds: A:E.43, A:D.75, A:D.75, A:D.75, A:R.148, A:E.201, A:R.216, A:R.216, A:Y.330 Water bridges: A:R.42, A:R.76, A:R.80, A:E.151, A:E.201, A:E.201 Salt bridges: A:R.42, A:R.216, A:R.295 SIA.10: 13 residues within 4Å: Chain B: R.42, E.43, D.75, R.76, W.102, R.148, A.170, E.200, E.201, R.216, N.218, R.295, Y.330 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:D.75, B:R.76 Hydrogen bonds: B:E.43, B:D.75, B:D.75, B:D.75, B:R.148, B:E.201, B:R.216, B:R.216, B:Y.330 Water bridges: B:R.42, B:R.76, B:R.80, B:E.151, B:E.201, B:E.201 Salt bridges: B:R.42, B:R.216, B:R.295 SIA.17: 13 residues within 4Å: Chain C: R.42, E.43, D.75, R.76, W.102, R.148, A.170, E.200, E.201, R.216, N.218, R.295, Y.330 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:D.75, C:R.76 Hydrogen bonds: C:E.43, C:D.75, C:D.75, C:D.75, C:R.148, C:E.201, C:R.216, C:R.216, C:Y.330 Water bridges: C:R.42, C:R.76, C:R.80, C:E.151, C:E.201, C:E.201 Salt bridges: C:R.42, C:R.216, C:R.295 SIA.24: 13 residues within 4Å: Chain D: R.42, E.43, D.75, R.76, W.102, R.148, A.170, E.200, E.201, R.216, N.218, R.295, Y.330 20 PLIP interactions: 20 interactions with chain D Hydrophobic interactions: D:D.75, D:R.76 Hydrogen bonds: D:E.43, D:D.75, D:D.75, D:D.75, D:R.148, D:E.201, D:R.216, D:R.216, D:Y.330 Water bridges: D:R.42, D:R.76, D:R.80, D:E.151, D:E.201, D:E.201 Salt bridges: D:R.42, D:R.216, D:R.295

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

MAN.4: 3 residues within 4Å: Chain C: D.254 Ligands: NAG-NAG-BMA-MAN-MAN.1, NAG-NAG-BMA-MAN-MAN.1 2 PLIP interactions: 2 interactions with chain C Water bridges: C:D.254, C:D.254 MAN.11: 3 residues within 4Å: Chain D: D.254 Ligands: NAG-NAG-BMA-MAN-MAN.8, NAG-NAG-BMA-MAN-MAN.8 2 PLIP interactions: 2 interactions with chain D Water bridges: D:D.254, D:D.254 MAN.18: 3 residues within 4Å: Chain B: D.254 Ligands: NAG-NAG-BMA-MAN-MAN.15, NAG-NAG-BMA-MAN-MAN.15 2 PLIP interactions: 2 interactions with chain B Water bridges: B:D.254, B:D.254 MAN.25: 3 residues within 4Å: Chain A: D.254 Ligands: NAG-NAG-BMA-MAN-MAN.22, NAG-NAG-BMA-MAN-MAN.22 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.254, A:D.254

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

SO4.5: 2 residues within 4Å: Chain A: H.74, D.75 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.75 Water bridges: A:R.76, A:R.76, A:R.76 Salt bridges: A:H.74 SO4.6: 3 residues within 4Å: Chain A: R.207, R.212, W.307 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.207, A:R.212 SO4.12: 2 residues within 4Å: Chain B: H.74, D.75 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.75 Water bridges: B:R.76, B:R.76, B:R.76 Salt bridges: B:H.74 SO4.13: 3 residues within 4Å: Chain B: R.207, R.212, W.307 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.207, B:R.212 SO4.19: 2 residues within 4Å: Chain C: H.74, D.75 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:D.75 Water bridges: C:R.76, C:R.76, C:R.76 Salt bridges: C:H.74 SO4.20: 3 residues within 4Å: Chain C: R.207, R.212, W.307 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:R.207, C:R.212 SO4.26: 2 residues within 4Å: Chain D: H.74, D.75 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:D.75 Water bridges: D:R.76, D:R.76, D:R.76 Salt bridges: D:H.74 SO4.27: 3 residues within 4Å: Chain D: R.207, R.212, W.307 2 PLIP interactions: 2 interactions with chain D Salt bridges: D:R.207, D:R.212

4 x CA: CALCIUM ION(Non-covalent)

CA.7: 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.5 CA.14: 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.14 CA.21: 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.23 CA.28: 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.33

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lei, R. et al., Mutational fitness landscape of human influenza H3N2 neuraminidase. Cell Rep (2023)

Release Date

2022-12-21

Peptides

Neuraminidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
AAA

C
AAA

D
AAA

Neuraminidase

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