SMTL ID : 4cpm.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

homo-tetramer

Ligands

2 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[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-MAN.1: 6 residues within 4Å: Chain A: E.79, Y.82, P.83, L.85, N.284 Ligands: NAG.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.79 NAG-NAG-BMA-MAN-MAN.18: 6 residues within 4Å: Chain C: E.79, Y.82, P.83, L.85, N.284 Ligands: NAG.21 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.79

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

NAG-NAG-BMA.2: 3 residues within 4Å: Chain B: Y.82, P.83, N.284 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.82 NAG-NAG-BMA.19: 3 residues within 4Å: Chain D: Y.82, P.83, N.284 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:Y.82

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 6 residues within 4Å: Chain A: D.293, T.297, A.298, 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.12: 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.4 CA.20: 6 residues within 4Å: Chain C: D.293, T.297, A.298, 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.29: 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.7

6 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-functional Binders)(Post Translational Modification)

NAG.4: 2 residues within 4Å: Ligands: NAG-NAG-BMA-MAN-MAN.1, NAG-NAG-BMA-MAN-MAN.1 No protein-ligand interaction detected (PLIP) NAG.5: 1 residues within 4Å: Chain A: N.144 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.144 NAG.13: 1 residues within 4Å: Chain B: N.144 No protein-ligand interaction detected (PLIP) NAG.21: 2 residues within 4Å: Ligands: NAG-NAG-BMA-MAN-MAN.18, NAG-NAG-BMA-MAN-MAN.18 No protein-ligand interaction detected (PLIP) NAG.22: 1 residues within 4Å: Chain C: N.144 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.144 NAG.30: 1 residues within 4Å: Chain D: N.144 No protein-ligand interaction detected (PLIP)

4 x G39: (3R,4R,5S)-4-(acetylamino)-5-amino-3-(pentan-3-yloxy)cyclohex-1-ene-1-carboxylic acid(Non-covalent)

G39.6: 13 residues within 4Å: Chain A: R.116, E.117, D.149, R.150, W.177, I.221, R.223, A.245, E.275, R.292, N.294, R.374, Y.409 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:W.177, A:I.221, A:A.245 Hydrogen bonds: A:D.149, A:D.149, A:R.150, A:Y.409 Water bridges: A:E.117, A:W.177, A:E.276, A:E.276 Salt bridges: A:R.116, A:R.292, A:R.374 G39.14: 15 residues within 4Å: Chain B: R.116, E.117, D.149, R.150, W.177, I.221, R.223, A.245, E.275, E.276, R.292, N.294, R.374, Y.409 Ligands: EDO.17 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:W.177, B:I.221, B:R.223, B:A.245 Hydrogen bonds: B:E.117, B:R.150, B:E.276, B:E.276, B:Y.409 Salt bridges: B:R.116, B:R.292, B:R.374 G39.23: 13 residues within 4Å: Chain C: R.116, E.117, D.149, R.150, W.177, I.221, R.223, A.245, E.275, R.292, N.294, R.374, Y.409 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:W.177, C:I.221, C:A.245 Hydrogen bonds: C:E.117, C:D.149, C:R.150 Water bridges: C:E.117, C:W.177, C:E.276 Salt bridges: C:R.116, C:R.292, C:R.374 G39.31: 15 residues within 4Å: Chain D: R.116, E.117, D.149, R.150, W.177, I.221, R.223, A.245, E.275, E.276, R.292, N.294, R.374, Y.409 Ligands: EDO.34 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:W.177, D:I.221, D:R.223, D:A.245 Hydrogen bonds: D:E.117, D:R.150, D:E.276 Salt bridges: D:R.116, D:R.292, D:R.374

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

EDO.7: 9 residues within 4Å: Chain A: R.102, F.103, E.105 Chain D: A.136, A.137, G.140, G.141, Y.142, Y.143 Ligand excluded by PLIP EDO.8: 2 residues within 4Å: Chain A: I.262, E.264 Ligand excluded by PLIP EDO.9: 8 residues within 4Å: Chain A: K.299, R.300, M.317, C.318, T.319, T.321, Y.322, L.323 Ligand excluded by PLIP EDO.10: 7 residues within 4Å: Chain A: Q.93, K.94, L.455, W.456 Chain D: D.194, L.201, K.203 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: G.108, N.109 Chain D: T.106, G.108, N.109 Ligand excluded by PLIP EDO.15: 9 residues within 4Å: Chain B: D.184, T.189, Y.206, G.234, C.236, I.256, R.257, E.258, G.259 Ligand excluded by PLIP EDO.16: 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.17: 7 residues within 4Å: Chain B: R.116, R.147, G.148, D.149, W.408, H.439 Ligands: G39.14 Ligand excluded by PLIP EDO.24: 9 residues within 4Å: Chain B: A.136, A.137, G.140, G.141, Y.142, Y.143 Chain C: R.102, F.103, E.105 Ligand excluded by PLIP EDO.25: 2 residues within 4Å: Chain C: I.262, E.264 Ligand excluded by PLIP EDO.26: 8 residues within 4Å: Chain C: K.299, R.300, M.317, C.318, T.319, T.321, Y.322, L.323 Ligand excluded by PLIP EDO.27: 7 residues within 4Å: Chain B: D.194, L.201, K.203 Chain C: Q.93, K.94, L.455, W.456 Ligand excluded by PLIP EDO.28: 5 residues within 4Å: Chain B: T.106, G.108, N.109 Chain C: G.108, N.109 Ligand excluded by PLIP EDO.32: 9 residues within 4Å: Chain D: D.184, T.189, Y.206, G.234, C.236, I.256, R.257, E.258, G.259 Ligand excluded by PLIP EDO.33: 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.34: 7 residues within 4Å: Chain D: R.116, R.147, G.148, D.149, W.408, H.439 Ligands: G39.31 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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