SMTL ID : 4gdi.1 (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

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

NAG-NAG-BMA-FUL-FUC.1: 6 residues within 4Å: Chain A: N.191, T.192, T.193, I.195, I.235 Ligands: GOL.11 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.195 Hydrogen bonds: A:I.235 Water bridges: A:I.235

1 x NAG- NAG- BMA- MAN- FUL- FUC: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG-BMA-MAN-FUL-FUC.2: 6 residues within 4Å: Chain B: N.191, T.192, T.193, G.194, I.195, I.235 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.195, B:I.235 Hydrogen bonds: B:I.235 Water bridges: B:I.235

1 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(Post Translational Modification)

NAG-FUL-NAG-FUC.3: 5 residues within 4Å: Chain C: N.191, T.192, T.193, I.195, I.235 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:I.195 Hydrogen bonds: C:I.235

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

NAG-NAG-FUC.4: 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

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

NAG.5: 4 residues within 4Å: Chain A: Y.8, Q.180, N.181 Chain D: I.331 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.181 Water bridges: A:Y.8, A:Y.8, A:Y.8 NAG.6: 2 residues within 4Å: Chain A: N.168, N.170 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.170 NAG.7: 2 residues within 4Å: Chain A: N.70 Chain D: P.32 No protein-ligand interaction detected (PLIP) NAG.14: 5 residues within 4Å: Chain A: I.331 Chain B: Y.8, Q.180, N.181, Q.185 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Q.180 Hydrogen bonds: B:N.181 Water bridges: B:Y.8, B:N.181 NAG.15: 2 residues within 4Å: Chain B: N.168, N.170 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.170 NAG.25: 4 residues within 4Å: Chain B: I.331 Chain C: Y.8, Q.180, N.181 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.8, C:N.181 NAG.26: 2 residues within 4Å: Chain B: P.32 Chain C: N.70 No protein-ligand interaction detected (PLIP) NAG.32: 6 residues within 4Å: Chain C: L.330, I.331 Chain D: Y.8, G.157, Q.180, N.181 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:Y.8, D:Q.180 Hydrogen bonds: D:Y.8, D:Q.180, C:L.330 Water bridges: D:Y.8, D:N.181, D:N.181 NAG.33: 2 residues within 4Å: Chain C: P.32 Chain D: N.70 2 PLIP interactions: 2 interactions with chain D Water bridges: D:N.70, D:N.70

7 x CA: CALCIUM ION(Non-covalent)

CA.8: 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.9 CA.16: 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.17: 3 residues within 4Å: Chain A: S.364 Chain B: D.135, T.136 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.135, H2O.14, H2O.19, H2O.19, H2O.19, H2O.19 CA.27: 8 residues within 4Å: Chain C: N.215, L.216, D.219, A.220, D.245, G.263, G.265, G.266 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:N.215, C:D.219, C:D.245, C:G.263, C:G.265 CA.28: 2 residues within 4Å: Chain B: N.363 Chain C: D.135 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:D.135, H2O.22, H2O.25, H2O.25, H2O.26 CA.34: 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.33 CA.35: 1 residues within 4Å: Chain D: Q.180 No protein-ligand interaction detected (PLIP)

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 15 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 B: E.131, E.132 Ligands: GOL.10, NO3.12 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:E.131, A:D.49, A:K.327, A:G.328, A:D.329, A:R.336 GOL.10: 14 residues within 4Å: Chain A: T.24, H.25, C.53, I.84, F.324, P.326, R.336, C.338, T.358, C.360 Chain B: K.128, E.131 Ligands: GOL.9, NO3.12 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:E.131, A:T.24 Hydrogen bonds: A:T.24 GOL.11: 8 residues within 4Å: Chain A: I.195, D.219, P.223, I.235, V.236, E.237, M.258 Ligands: NAG-NAG-BMA-FUL-FUC.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.237 Water bridges: A:D.219 GOL.18: 10 residues within 4Å: Chain B: M.15, C.16, E.17, V.18, L.272, E.274, K.275, P.276, W.278, Q.295 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:V.18, B:V.18, B:V.18, B:W.278, B:Q.295 GOL.19: 12 residues within 4Å: Chain B: G.27, F.28, P.29, W.30, K.316, I.343, D.345, E.355, S.357 Chain C: S.72, E.76 Ligands: NO3.21 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:F.28, B:K.316, B:D.345 Water bridges: B:D.372, C:S.72 GOL.29: 13 residues within 4Å: Chain C: 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 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:D.49, C:K.327, C:G.328, C:D.329, C:D.329, C:R.336, D:E.131 Water bridges: C:R.336 GOL.36: 12 residues within 4Å: Chain A: S.72, E.76 Chain D: R.26, G.27, F.28, P.29, W.30, K.316, I.343, D.345, E.355 Ligands: NO3.38 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:G.27, D:K.316, D:D.345, D:D.345 Water bridges: D:G.27, D:G.27, A:E.76

11 x NO3: NITRATE ION(Non-functional Binders)

NO3.12: 10 residues within 4Å: Chain A: T.24, P.326, R.336, C.360 Chain B: K.128, E.131, E.132, V.133 Ligands: GOL.9, GOL.10 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:V.133, A:T.24, A:T.24, A:R.336, A:R.336 NO3.13: 5 residues within 4Å: Chain A: N.149, Y.199, I.267, Q.268, R.320 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.199, A:Q.268, A:R.320 Water bridges: A:N.149 NO3.20: 5 residues within 4Å: Chain B: N.149, Y.199, I.267, Q.268, R.320 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.199, B:Q.268, B:R.320 NO3.21: 10 residues within 4Å: Chain B: R.26, G.27, F.313, K.316, I.343, S.357, F.359, W.371 Chain C: E.76 Ligands: GOL.19 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.26, B:R.26, B:K.316, B:S.357, B:S.357 Water bridges: B:G.27 NO3.22: 8 residues within 4Å: Chain B: S.41, R.42, A.44, K.55, E.342, Q.354, E.355, L.356 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.41, B:K.55, B:E.355, B:E.355, B:L.356 Water bridges: B:E.342 NO3.23: 5 residues within 4Å: Chain B: F.137, Y.177, V.184, W.187 Ligands: NO3.24 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.187 Water bridges: B:T.136 NO3.24: 3 residues within 4Å: Chain B: R.175, W.187 Ligands: NO3.23 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:W.187 Water bridges: B:R.175, B:R.175, B:Y.177 NO3.30: 4 residues within 4Å: Chain C: Y.199, I.267, Q.268, R.320 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Y.199, C:Q.268, C:R.320 Water bridges: C:Q.268 NO3.31: 4 residues within 4Å: Chain C: F.137, Y.177, V.184, W.187 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:W.187 Water bridges: C:V.184 NO3.37: 4 residues within 4Å: Chain D: Y.199, I.267, Q.268, R.320 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:Y.199, D:Q.268, D:Q.268, D:R.320 Water bridges: D:Y.199, D:G.266 NO3.38: 10 residues within 4Å: Chain A: E.76 Chain D: R.26, G.27, F.313, K.316, I.343, S.357, F.359, W.371 Ligands: GOL.36 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:R.26, D:R.26, D:G.27, D:K.316, D:S.357, D:S.357

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
A

B
B

C
C

D
D

Neuraminidase

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