SMTL ID : 4gdi.2 (2 other biounits)

A subtype N10 neuraminidase-like protein of A/little yellow-shouldered bat/Guatemala/164/2009

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-tetramer

Ligands

4 x NAG- FUL- NAG- FUC: beta-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-FUL-NAG-FUC.1: 5 residues within 4Å: Chain A: N.191, T.192, T.193, I.195, I.235 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.195 Hydrogen bonds: A:I.235 Water bridges: A:I.235 NAG-FUL-NAG-FUC.10: 5 residues within 4Å: Chain B: N.191, T.192, T.193, I.195, I.235 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.195 Hydrogen bonds: B:I.235 Water bridges: B:I.235 NAG-FUL-NAG-FUC.19: 5 residues within 4Å: Chain C: N.191, T.192, T.193, I.195, I.235 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:I.195 Hydrogen bonds: C:I.235 Water bridges: C:I.235 NAG-FUL-NAG-FUC.28: 5 residues within 4Å: Chain D: N.191, T.192, T.193, I.195, I.235 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:I.195 Hydrogen bonds: D:I.235 Water bridges: D:I.235

4 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.2: 4 residues within 4Å: Chain A: N.168, V.169, N.170, E.264 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.264, A:N.170 NAG-FUC.11: 4 residues within 4Å: Chain B: N.168, V.169, N.170, E.264 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.264, B:N.170 NAG-FUC.20: 4 residues within 4Å: Chain C: N.168, V.169, N.170, E.264 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.264, C:N.170 NAG-FUC.29: 4 residues within 4Å: Chain D: N.168, V.169, N.170, E.264 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.264, D:N.170

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

NAG.3: 6 residues within 4Å: Chain A: Y.8, G.157, Q.180, N.181 Chain C: I.331 Ligands: GOL.7 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.8, A:Q.180 Hydrogen bonds: A:Y.8, A:Q.180 Water bridges: A:Y.8 NAG.4: 2 residues within 4Å: Chain A: N.70 Chain C: P.32 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.70 NAG.12: 6 residues within 4Å: Chain B: Y.8, G.157, Q.180, N.181 Chain D: I.331 Ligands: GOL.16 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Y.8, B:Q.180 Hydrogen bonds: B:Y.8, B:Q.180 Water bridges: B:Y.8 NAG.13: 2 residues within 4Å: Chain B: N.70 Chain D: P.32 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.70 NAG.21: 6 residues within 4Å: Chain B: I.331 Chain C: Y.8, G.157, Q.180, N.181 Ligands: GOL.25 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:Y.8, C:Q.180 Hydrogen bonds: C:Y.8, C:Q.180 Water bridges: C:Y.8 NAG.22: 2 residues within 4Å: Chain B: P.32 Chain C: N.70 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.70 NAG.30: 6 residues within 4Å: Chain A: I.331 Chain D: Y.8, G.157, Q.180, N.181 Ligands: GOL.34 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:Y.8, D:Q.180 Hydrogen bonds: D:Y.8, D:Q.180 Water bridges: D:Y.8 NAG.31: 2 residues within 4Å: Chain A: P.32 Chain D: N.70 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.70

8 x CA: CALCIUM ION(Non-covalent)

CA.5: 8 residues within 4Å: Chain A: N.215, L.216, D.219, A.220, D.245, G.263, G.265, G.266 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:N.215, A:D.219, A:D.245, A:G.263, A:G.265, H2O.7 CA.6: 3 residues within 4Å: Chain A: S.158, E.178, Q.180 No protein-ligand interaction detected (PLIP) CA.14: 8 residues within 4Å: Chain B: N.215, L.216, D.219, A.220, D.245, G.263, G.265, G.266 6 PLIP interactions: 5 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:N.215, B:D.219, B:D.245, B:G.263, B:G.265, H2O.15 CA.15: 3 residues within 4Å: Chain B: S.158, E.178, Q.180 No protein-ligand interaction detected (PLIP) CA.23: 8 residues within 4Å: Chain C: N.215, L.216, D.219, A.220, D.245, G.263, G.265, G.266 6 PLIP interactions: 5 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:N.215, C:D.219, C:D.245, C:G.263, C:G.265, H2O.23 CA.24: 3 residues within 4Å: Chain C: S.158, E.178, Q.180 No protein-ligand interaction detected (PLIP) CA.32: 8 residues within 4Å: Chain D: N.215, L.216, D.219, A.220, D.245, G.263, G.265, G.266 6 PLIP interactions: 5 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:N.215, D:D.219, D:D.245, D:G.263, D:G.265, H2O.31 CA.33: 3 residues within 4Å: Chain D: S.158, E.178, Q.180 No protein-ligand interaction detected (PLIP)

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 6 residues within 4Å: Chain A: Q.180, N.181, T.183, Q.185 Chain C: I.331 Ligands: NAG.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.180, A:N.181 GOL.8: 13 residues within 4Å: Chain A: C.48, D.49, L.50, T.51, S.52, C.53, P.326, K.327, G.328, D.329, R.336 Chain D: E.131, E.132 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.49, A:K.327, A:G.328, A:D.329 GOL.9: 1 residues within 4Å: Chain A: E.17 No protein-ligand interaction detected (PLIP) GOL.16: 6 residues within 4Å: Chain B: Q.180, N.181, T.183, Q.185 Chain D: I.331 Ligands: NAG.12 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.180, B:N.181 GOL.17: 13 residues within 4Å: Chain B: C.48, D.49, L.50, T.51, S.52, C.53, P.326, K.327, G.328, D.329, R.336 Chain C: E.131, E.132 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.49, B:K.327, B:G.328, B:D.329 GOL.18: 1 residues within 4Å: Chain B: E.17 No protein-ligand interaction detected (PLIP) GOL.25: 6 residues within 4Å: Chain B: I.331 Chain C: Q.180, N.181, T.183, Q.185 Ligands: NAG.21 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.180, C:N.181 GOL.26: 13 residues within 4Å: Chain A: E.131, E.132 Chain C: C.48, D.49, L.50, T.51, S.52, C.53, P.326, K.327, G.328, D.329, R.336 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.49, C:K.327, C:G.328, C:D.329 GOL.27: 1 residues within 4Å: Chain C: E.17 No protein-ligand interaction detected (PLIP) GOL.34: 6 residues within 4Å: Chain A: I.331 Chain D: Q.180, N.181, T.183, Q.185 Ligands: NAG.30 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.180, D:N.181 GOL.35: 13 residues within 4Å: Chain B: E.131, E.132 Chain D: C.48, D.49, L.50, T.51, S.52, C.53, P.326, K.327, G.328, D.329, R.336 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.49, D:K.327, D:G.328, D:D.329 GOL.36: 1 residues within 4Å: Chain D: E.17 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhu, X. et al., Crystal structures of two subtype N10 neuraminidase-like proteins from bat influenza A viruses reveal a diverged putative active site. Proc.Natl.Acad.Sci.USA (2012)

Release Date

2012-09-26

Peptides

Neuraminidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
E

C
E

D
E

Neuraminidase

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