SMTL ID : 3w09.1

Influenza virus neuraminidase subtype N9 (TERN) complexed with 2,3-dif guanidino-neu5ac2en inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 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.119, N.120 Chain C: R.247, N.249, D.250, R.283, I.285, I.287, E.294, L.296, K.308, P.309, T.310, Q.311, G.312, F.372, L.373, G.374, Q.375 7 PLIP interactions: 7 interactions with chain C Water bridges: C:Q.313, C:Q.311, C:G.312, C:T.314 Hydrophobic interactions: C:F.372 Hydrogen bonds: C:G.312, C:G.312, C:Q.375 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.13: 19 residues within 4Å: Chain B: N.119, N.120 Chain D: R.247, N.249, D.250, R.283, I.285, I.287, E.294, L.296, K.308, P.309, T.310, Q.311, G.312, F.372, L.373, G.374, Q.375 7 PLIP interactions: 7 interactions with chain D Water bridges: D:Q.313, D:Q.311, D:G.312, D:T.314 Hydrophobic interactions: D:F.372 Hydrogen bonds: D:G.312, D:G.312, D:Q.375 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.25: 19 residues within 4Å: Chain B: R.247, N.249, D.250, R.283, I.285, I.287, E.294, L.296, K.308, P.309, T.310, Q.311, G.312, F.372, L.373, G.374, Q.375 Chain C: N.119, N.120 7 PLIP interactions: 7 interactions with chain B Water bridges: B:Q.313, B:Q.311, B:G.312, B:T.314 Hydrophobic interactions: B:F.372 Hydrogen bonds: B:G.312, B:G.312, B:Q.375 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.37: 19 residues within 4Å: Chain A: R.247, N.249, D.250, R.283, I.285, I.287, E.294, L.296, K.308, P.309, T.310, Q.311, G.312, F.372, L.373, G.374, Q.375 Chain D: N.119, N.120 7 PLIP interactions: 7 interactions with chain A Water bridges: A:Q.313, A:Q.311, A:G.312, A:T.314 Hydrophobic interactions: A:F.372 Hydrogen bonds: A:G.312, A:G.312, A:Q.375

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.2, F.3, N.5, N.154 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain B: D.2, F.3, N.5, N.154 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 4 residues within 4Å: Chain C: D.2, F.3, N.5, N.154 No protein-ligand interaction detected (PLIP) NAG-NAG.38: 4 residues within 4Å: Chain D: D.2, F.3, N.5, N.154 No protein-ligand interaction detected (PLIP)

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

NAG.3: 2 residues within 4Å: Chain A: N.65, W.357 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.65, A:W.357 NAG.15: 2 residues within 4Å: Chain B: N.65, W.357 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.65, B:W.357 NAG.27: 2 residues within 4Å: Chain C: N.65, W.357 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.65, C:W.357 NAG.39: 2 residues within 4Å: Chain D: N.65, W.357 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.65, D:W.357

28 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: H.63, N.65, G.66, T.67, S.72, Y.74 Chain C: R.26 Ligand excluded by PLIP GOL.5: 6 residues within 4Å: Chain A: C.11, A.333, E.334, G.335, C.337, R.339 Ligand excluded by PLIP GOL.6: 12 residues within 4Å: Chain A: L.34, S.54, G.56, Y.74, R.75, A.76, I.96 Chain C: K.21, D.22, N.23, I.27, S.83 Ligand excluded by PLIP GOL.7: 5 residues within 4Å: Chain A: L.188, A.189, G.190, A.192, K.193 Ligand excluded by PLIP GOL.8: 4 residues within 4Å: Chain A: S.286, A.288, S.289, N.318 Ligand excluded by PLIP GOL.9: 4 residues within 4Å: Chain A: K.255, C.256, N.257, D.258 Ligand excluded by PLIP GOL.10: 3 residues within 4Å: Chain A: H.69, D.70, R.71 Ligand excluded by PLIP GOL.16: 7 residues within 4Å: Chain B: H.63, N.65, G.66, T.67, S.72, Y.74 Chain D: R.26 Ligand excluded by PLIP GOL.17: 6 residues within 4Å: Chain B: C.11, A.333, E.334, G.335, C.337, R.339 Ligand excluded by PLIP GOL.18: 12 residues within 4Å: Chain B: L.34, S.54, G.56, Y.74, R.75, A.76, I.96 Chain D: K.21, D.22, N.23, I.27, S.83 Ligand excluded by PLIP GOL.19: 5 residues within 4Å: Chain B: L.188, A.189, G.190, A.192, K.193 Ligand excluded by PLIP GOL.20: 4 residues within 4Å: Chain B: S.286, A.288, S.289, N.318 Ligand excluded by PLIP GOL.21: 4 residues within 4Å: Chain B: K.255, C.256, N.257, D.258 Ligand excluded by PLIP GOL.22: 3 residues within 4Å: Chain B: H.69, D.70, R.71 Ligand excluded by PLIP GOL.28: 7 residues within 4Å: Chain B: R.26 Chain C: H.63, N.65, G.66, T.67, S.72, Y.74 Ligand excluded by PLIP GOL.29: 6 residues within 4Å: Chain C: C.11, A.333, E.334, G.335, C.337, R.339 Ligand excluded by PLIP GOL.30: 12 residues within 4Å: Chain B: K.21, D.22, N.23, I.27, S.83 Chain C: L.34, S.54, G.56, Y.74, R.75, A.76, I.96 Ligand excluded by PLIP GOL.31: 5 residues within 4Å: Chain C: L.188, A.189, G.190, A.192, K.193 Ligand excluded by PLIP GOL.32: 4 residues within 4Å: Chain C: S.286, A.288, S.289, N.318 Ligand excluded by PLIP GOL.33: 4 residues within 4Å: Chain C: K.255, C.256, N.257, D.258 Ligand excluded by PLIP GOL.34: 3 residues within 4Å: Chain C: H.69, D.70, R.71 Ligand excluded by PLIP GOL.40: 7 residues within 4Å: Chain A: R.26 Chain D: H.63, N.65, G.66, T.67, S.72, Y.74 Ligand excluded by PLIP GOL.41: 6 residues within 4Å: Chain D: C.11, A.333, E.334, G.335, C.337, R.339 Ligand excluded by PLIP GOL.42: 12 residues within 4Å: Chain A: K.21, D.22, N.23, I.27, S.83 Chain D: L.34, S.54, G.56, Y.74, R.75, A.76, I.96 Ligand excluded by PLIP GOL.43: 5 residues within 4Å: Chain D: L.188, A.189, G.190, A.192, K.193 Ligand excluded by PLIP GOL.44: 4 residues within 4Å: Chain D: S.286, A.288, S.289, N.318 Ligand excluded by PLIP GOL.45: 4 residues within 4Å: Chain D: K.255, C.256, N.257, D.258 Ligand excluded by PLIP GOL.46: 3 residues within 4Å: Chain D: H.69, D.70, R.71 Ligand excluded by PLIP

4 x ZGE: 5-acetamido-2,6-anhydro-4-carbamimidamido-3,4,5-trideoxy-3-fluoro-D-glycero-D-galacto-non-2-enonic acid(Post Translational Modification)

ZGE.11: 15 residues within 4Å: Chain A: R.37, E.38, D.70, R.71, R.75, W.98, I.142, R.144, E.147, A.166, E.196, E.197, R.212, R.290, Y.324 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:W.98, A:I.142, A:R.144 Hydrogen bonds: A:R.71, A:W.98, A:W.98, A:E.197, A:R.212 Water bridges: A:R.37, A:R.75, A:R.144, A:E.147, A:E.197, A:E.197, A:R.212, A:R.212 Salt bridges: A:R.37, A:E.38, A:D.70, A:E.147, A:R.212, A:R.290 Halogen bonds: A:R.37 ZGE.23: 15 residues within 4Å: Chain B: R.37, E.38, D.70, R.71, R.75, W.98, I.142, R.144, E.147, A.166, E.196, E.197, R.212, R.290, Y.324 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:W.98, B:I.142, B:R.144 Hydrogen bonds: B:R.71, B:W.98, B:W.98, B:E.197, B:R.212 Water bridges: B:R.37, B:R.75, B:R.144, B:E.147, B:E.197, B:E.197, B:R.212, B:R.212 Salt bridges: B:R.37, B:E.38, B:D.70, B:E.147, B:R.212, B:R.290 Halogen bonds: B:R.37 ZGE.35: 15 residues within 4Å: Chain C: R.37, E.38, D.70, R.71, R.75, W.98, I.142, R.144, E.147, A.166, E.196, E.197, R.212, R.290, Y.324 23 PLIP interactions: 23 interactions with chain C Hydrophobic interactions: C:W.98, C:I.142, C:R.144 Hydrogen bonds: C:R.71, C:W.98, C:W.98, C:E.197, C:R.212 Water bridges: C:R.37, C:R.75, C:R.144, C:E.147, C:E.197, C:E.197, C:R.212, C:R.212 Salt bridges: C:R.37, C:E.38, C:D.70, C:E.147, C:R.212, C:R.290 Halogen bonds: C:R.37 ZGE.47: 15 residues within 4Å: Chain D: R.37, E.38, D.70, R.71, R.75, W.98, I.142, R.144, E.147, A.166, E.196, E.197, R.212, R.290, Y.324 23 PLIP interactions: 23 interactions with chain D Hydrophobic interactions: D:W.98, D:I.142, D:R.144 Hydrogen bonds: D:R.71, D:W.98, D:W.98, D:E.197, D:R.212 Water bridges: D:R.37, D:R.75, D:R.144, D:E.147, D:E.197, D:E.197, D:R.212, D:R.212 Salt bridges: D:R.37, D:E.38, D:D.70, D:E.147, D:R.212, D:R.290 Halogen bonds: D:R.37

4 x CA: CALCIUM ION(Non-covalent)

CA.12: 5 residues within 4Å: Chain A: D.213, G.217, D.244, N.266, G.267 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.213, A:G.217, A:D.244, H2O.7, H2O.9 CA.24: 5 residues within 4Å: Chain B: D.213, G.217, D.244, N.266, G.267 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.213, B:G.217, B:D.244, H2O.21, H2O.24 CA.36: 5 residues within 4Å: Chain C: D.213, G.217, D.244, N.266, G.267 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.213, C:G.217, C:D.244, H2O.36, H2O.39 CA.48: 5 residues within 4Å: Chain D: D.213, G.217, D.244, N.266, G.267 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.213, D:G.217, D:D.244, H2O.51, H2O.54

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, J.-H. et al., Mechanism-based covalent neuraminidase inhibitors with broad-spectrum influenza antiviral activity. Science (2013)

Release Date

2013-05-01

Peptides

Neuraminidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Neuraminidase

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