SMTL ID : 4cpn.1

Structure of the Neuraminidase from the B/Brisbane/60/2008 virus in complex with Zanamivir

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

2 x NAG- NAG- BMA- MAN: 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(Non-covalent)

NAG-NAG-BMA-MAN.1: 5 residues within 4Å: Chain A: E.79, Y.82, P.83, L.85, N.284 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.16: 5 residues within 4Å: Chain C: E.79, Y.82, P.83, L.85, N.284 No protein-ligand interaction detected (PLIP)

2 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: 1 residues within 4Å: Chain A: N.144 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 1 residues within 4Å: Chain C: N.144 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG-BMA.3: 4 residues within 4Å: Chain B: Y.82, P.83, L.85, N.284 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.82 NAG-NAG-BMA.18: 4 residues within 4Å: Chain D: Y.82, P.83, L.85, N.284 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:Y.82

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.8: 5 residues within 4Å: Chain B: D.293, T.297, D.324, G.344, G.346 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.293, B:T.297, B:D.324, B:G.344, B:G.346 CA.19: 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.23: 5 residues within 4Å: Chain D: D.293, T.297, D.324, G.344, G.346 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.293, D:T.297, D:D.324, D:G.344, D:G.346

4 x ZMR: ZANAMIVIR(Non-covalent)

ZMR.5: 16 residues within 4Å: Chain A: R.116, E.117, D.149, R.150, R.154, W.177, I.221, R.223, E.226, A.245, E.275, E.276, R.292, N.294, R.374, Y.409 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:W.177, A:I.221, A:R.223 Hydrogen bonds: A:R.150, A:W.177, A:W.177, A:R.223, A:E.276, A:E.276, A:R.292, A:R.292 Water bridges: A:R.116, A:D.149, A:R.150, A:R.154, A:E.226, A:R.374 Salt bridges: A:R.116, A:E.117, A:D.149, A:E.226, A:R.292, A:R.374 ZMR.10: 14 residues within 4Å: Chain B: R.116, E.117, D.149, R.150, R.154, W.177, R.223, E.226, A.245, E.275, E.276, R.292, R.374, Y.409 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:D.149, B:R.150 Hydrogen bonds: B:D.149, B:D.149, B:W.177, B:R.223, B:E.276, B:E.276, B:E.276, B:R.292, B:R.292 Water bridges: B:R.116, B:R.154 Salt bridges: B:R.116, B:E.117, B:D.149, B:E.226, B:R.292, B:R.374 ZMR.20: 16 residues within 4Å: Chain C: R.116, E.117, D.149, R.150, R.154, W.177, I.221, R.223, E.226, A.245, E.275, E.276, R.292, N.294, R.374, Y.409 24 PLIP interactions: 24 interactions with chain C Hydrophobic interactions: C:W.177, C:I.221, C:R.223 Hydrogen bonds: C:R.150, C:W.177, C:W.177, C:R.223, C:E.276, C:E.276, C:E.276, C:R.292, C:R.292, C:Y.409 Water bridges: C:R.116, C:D.149, C:R.150, C:R.154, C:R.374 Salt bridges: C:R.116, C:E.117, C:D.149, C:E.226, C:R.292, C:R.374 ZMR.25: 14 residues within 4Å: Chain D: R.116, E.117, D.149, R.150, R.154, W.177, R.223, E.226, A.245, E.275, E.276, R.292, R.374, Y.409 19 PLIP interactions: 19 interactions with chain D Hydrophobic interactions: D:D.149, D:R.150 Hydrogen bonds: D:D.149, D:D.149, D:W.177, D:R.223, D:E.276, D:E.276, D:R.292, D:R.292, D:Y.409 Water bridges: D:R.116, D:R.154 Salt bridges: D:R.116, D:E.117, D:D.149, D:E.226, D:R.292, D:R.374

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

EDO.6: 9 residues within 4Å: Chain A: A.136, A.137, G.140, G.141, Y.142, Y.143 Chain D: R.102, F.103, E.105 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A Water bridges: D:F.103, D:E.105 Hydrogen bonds: A:A.137, A:Y.142 EDO.7: 9 residues within 4Å: Chain A: D.184, T.189, Y.206, G.234, C.236, I.256, R.257, E.258, G.259 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.184, A:E.258, A:G.259 EDO.11: 7 residues within 4Å: Chain B: Q.93, K.94, L.455, W.456 Chain C: D.194, L.201, K.203 6 PLIP interactions: 2 interactions with chain C, 4 interactions with chain B Hydrogen bonds: C:K.203, C:K.203, B:Q.93, B:K.94, B:L.455, B:W.456 EDO.12: 9 residues within 4Å: Chain B: C.122, G.123, P.124, N.125, E.126, C.127, I.415, K.416 Chain C: E.208 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.124, B:K.416 EDO.13: 10 residues within 4Å: Chain A: K.94, W.456 Chain B: N.151, K.152, L.153, R.154, A.175, A.176, W.177, D.194 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:A.176, B:A.176, A:K.94, A:K.94 EDO.14: 7 residues within 4Å: Chain A: R.102 Chain B: H.134, Y.142, N.144, T.146, N.151, L.153 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.134, B:Y.142, B:N.151, A:R.102 EDO.15: 8 residues within 4Å: Chain B: K.299, R.300, M.317, C.318, T.319, T.321, Y.322, L.323 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.300, B:T.319, B:L.323 EDO.21: 9 residues within 4Å: Chain B: R.102, F.103, E.105 Chain C: A.136, A.137, G.140, G.141, Y.142, Y.143 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:A.137, C:Y.142 Water bridges: B:F.103, B:E.105 EDO.22: 9 residues within 4Å: Chain C: D.184, T.189, Y.206, G.234, C.236, I.256, R.257, E.258, G.259 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:D.184, C:D.184, C:T.189, C:E.258, C:G.259 EDO.26: 7 residues within 4Å: Chain A: D.194, L.201, K.203 Chain D: Q.93, K.94, L.455, W.456 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:Q.93, D:K.94, D:L.455, D:W.456, A:K.203, A:K.203 EDO.27: 9 residues within 4Å: Chain A: E.208 Chain D: C.122, G.123, P.124, N.125, E.126, C.127, I.415, K.416 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:P.124, D:K.416 EDO.28: 10 residues within 4Å: Chain C: K.94, W.456 Chain D: N.151, K.152, L.153, R.154, A.175, A.176, W.177, D.194 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:K.94, C:K.94, D:A.176, D:A.176, D:D.194 EDO.29: 7 residues within 4Å: Chain C: R.102 Chain D: H.134, Y.142, N.144, T.146, N.151, L.153 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:R.102, D:Y.142, D:N.151 EDO.30: 8 residues within 4Å: Chain D: K.299, R.300, M.317, C.318, T.319, T.321, Y.322, L.323 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.300, D:T.319, D:L.323

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

NAG.9: 2 residues within 4Å: Chain B: N.144, G.145 No protein-ligand interaction detected (PLIP) NAG.24: 2 residues within 4Å: Chain D: N.144, G.145 No protein-ligand interaction detected (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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