SMTL ID : 4cpo.1

Structure of the Neuraminidase from the B/Lyon/CHU/15.216/2011 virus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

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.1: 5 residues within 4Å: Chain A: Y.82, P.83, R.84, L.85, N.284 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.82 NAG-NAG.2: 4 residues within 4Å: Chain B: E.79, Y.82, P.83, N.284 1 PLIP interactions: 1 interactions with chain B Water bridges: B:E.79 NAG-NAG.27: 5 residues within 4Å: Chain C: Y.82, P.83, R.84, L.85, N.284 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.82 NAG-NAG.28: 4 residues within 4Å: Chain D: E.79, Y.82, P.83, N.284 No protein-ligand interaction detected (PLIP)

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

NAG.3: 1 residues within 4Å: Chain A: N.144 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.144 Water bridges: A:N.144 NAG.17: 1 residues within 4Å: Chain B: N.144 No protein-ligand interaction detected (PLIP) NAG.29: 1 residues within 4Å: Chain C: N.144 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.144 Water bridges: C:N.144 NAG.43: 1 residues within 4Å: Chain D: N.144 1 PLIP interactions: 1 interactions with chain D Water bridges: D:E.436

4 x CA: CALCIUM ION(Non-covalent)

CA.4: 5 residues within 4Å: Chain A: D.293, T.297, D.324, G.344, G.346 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.293, A:T.297, A:D.324, A:G.344, A:G.346 CA.18: 5 residues within 4Å: Chain B: D.293, T.297, D.324, G.344, G.346 6 PLIP interactions: 5 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.293, B:T.297, B:D.324, B:G.344, B:G.346, H2O.20 CA.30: 5 residues within 4Å: Chain C: D.293, T.297, D.324, G.344, G.346 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.293, C:T.297, C:D.324, C:G.344, C:G.346 CA.44: 5 residues within 4Å: Chain D: D.293, T.297, D.324, G.344, G.346 6 PLIP interactions: 5 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.293, D:T.297, D:D.324, D:G.344, D:G.346, H2O.43

40 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 9 residues within 4Å: Chain A: C.122, G.123, P.124, N.125, E.126, C.127, I.415, K.416 Chain D: E.208 Ligand excluded by PLIP EDO.6: 4 residues within 4Å: Chain A: P.88, E.419, C.420 Chain D: R.260 Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain A: P.88, G.450 Chain D: T.211, D.212, R.260 Ligand excluded by PLIP EDO.8: 8 residues within 4Å: Chain A: R.102 Chain D: H.134, Y.142, N.144, G.145, T.146, N.151, L.153 Ligand excluded by PLIP EDO.9: 7 residues within 4Å: Chain A: Y.143, N.144, G.145, T.146, R.147, G.148, K.435 Ligand excluded by PLIP EDO.10: 8 residues within 4Å: Chain A: H.134, Y.142, N.144, G.145, T.146, N.151, L.153 Chain B: R.102 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: D.149, R.150, W.177, R.223, E.226 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain A: Y.217, E.250, C.251, R.252, F.266, P.267 Ligand excluded by PLIP EDO.13: 3 residues within 4Å: Chain A: D.320, D.392, A.393 Ligand excluded by PLIP EDO.14: 3 residues within 4Å: Chain A: K.371, T.372 Ligands: EDO.15 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain A: D.329, K.371 Ligands: EDO.14 Ligand excluded by PLIP EDO.16: 2 residues within 4Å: Chain A: G.385, D.386 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain A: R.260 Chain B: P.88, E.419, C.420 Ligand excluded by PLIP EDO.20: 9 residues within 4Å: Chain A: E.208 Chain B: C.122, G.123, P.124, N.125, E.126, C.127, I.415, K.416 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain B: S.90, T.91, V.381, S.397, G.452, Q.453 Ligand excluded by PLIP EDO.22: 7 residues within 4Å: Chain B: Y.143, N.144, G.145, T.146, R.147, G.148, K.435 Ligand excluded by PLIP EDO.23: 6 residues within 4Å: Chain B: A.245, E.275, E.276, R.292, N.294 Ligands: EDO.24 Ligand excluded by PLIP EDO.24: 4 residues within 4Å: Chain B: D.149, R.150, W.177 Ligands: EDO.23 Ligand excluded by PLIP EDO.25: 4 residues within 4Å: Chain B: R.147, D.432, G.433, G.434 Ligand excluded by PLIP EDO.26: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.31: 9 residues within 4Å: Chain B: E.208 Chain C: C.122, G.123, P.124, N.125, E.126, C.127, I.415, K.416 Ligand excluded by PLIP EDO.32: 4 residues within 4Å: Chain B: R.260 Chain C: P.88, E.419, C.420 Ligand excluded by PLIP EDO.33: 5 residues within 4Å: Chain B: T.211, D.212, R.260 Chain C: P.88, G.450 Ligand excluded by PLIP EDO.34: 8 residues within 4Å: Chain B: H.134, Y.142, N.144, G.145, T.146, N.151, L.153 Chain C: R.102 Ligand excluded by PLIP EDO.35: 7 residues within 4Å: Chain C: Y.143, N.144, G.145, T.146, R.147, G.148, K.435 Ligand excluded by PLIP EDO.36: 8 residues within 4Å: Chain C: H.134, Y.142, N.144, G.145, T.146, N.151, L.153 Chain D: R.102 Ligand excluded by PLIP EDO.37: 5 residues within 4Å: Chain C: D.149, R.150, W.177, R.223, E.226 Ligand excluded by PLIP EDO.38: 6 residues within 4Å: Chain C: Y.217, E.250, C.251, R.252, F.266, P.267 Ligand excluded by PLIP EDO.39: 3 residues within 4Å: Chain C: D.320, D.392, A.393 Ligand excluded by PLIP EDO.40: 3 residues within 4Å: Chain C: K.371, T.372 Ligands: EDO.41 Ligand excluded by PLIP EDO.41: 3 residues within 4Å: Chain C: D.329, K.371 Ligands: EDO.40 Ligand excluded by PLIP EDO.42: 2 residues within 4Å: Chain C: G.385, D.386 Ligand excluded by PLIP EDO.45: 4 residues within 4Å: Chain C: R.260 Chain D: P.88, E.419, C.420 Ligand excluded by PLIP EDO.46: 9 residues within 4Å: Chain C: E.208 Chain D: C.122, G.123, P.124, N.125, E.126, C.127, I.415, K.416 Ligand excluded by PLIP EDO.47: 6 residues within 4Å: Chain D: S.90, T.91, V.381, S.397, G.452, Q.453 Ligand excluded by PLIP EDO.48: 7 residues within 4Å: Chain D: Y.143, N.144, G.145, T.146, R.147, G.148, K.435 Ligand excluded by PLIP EDO.49: 6 residues within 4Å: Chain D: A.245, E.275, E.276, R.292, N.294 Ligands: EDO.50 Ligand excluded by PLIP EDO.50: 4 residues within 4Å: Chain D: D.149, R.150, W.177 Ligands: EDO.49 Ligand excluded by PLIP EDO.51: 4 residues within 4Å: Chain D: R.147, D.432, G.433, G.434 Ligand excluded by PLIP EDO.52: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Escuret, V. et al., A Novel I221 L Substitution in Neuraminidase Confers High Level Resistance to Oseltamivir in Influenza B Viruses. J.Infect.Dis. (2014)

Release Date

2014-05-14

Peptides

NEURAMINIDASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

NEURAMINIDASE

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