SMTL ID : 3k39.4 (3 other biounits)

Crystal Structure of B/Perth Neuraminidase D197E mutant in complex with Peramivir

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.54 Å

Oligo State

homo-tetramer

Ligands

1 x YT3: YTTRIUM (III) ION(Non-covalent)

YT3.1: 4 residues within 4Å: Chain A: E.99 Chain B: E.99 Chain C: E.99 Chain D: E.99 No protein-ligand interaction detected (PLIP)

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

NAG.2: 4 residues within 4Å: Chain A: P.14, R.15, L.16, N.215 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.16 Hydrogen bonds: A:P.14 NAG.5: 4 residues within 4Å: Chain B: P.14, R.15, L.16, N.215 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.16 Hydrogen bonds: B:P.14 NAG.8: 4 residues within 4Å: Chain C: P.14, R.15, L.16, N.215 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.16 Hydrogen bonds: C:P.14 NAG.11: 4 residues within 4Å: Chain D: P.14, R.15, L.16, N.215 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:L.16 Hydrogen bonds: D:P.14

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 6 residues within 4Å: Chain A: D.224, T.228, D.255, G.275, G.277, G.278 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.224, A:T.228, A:D.255, A:G.275, A:G.277 CA.6: 5 residues within 4Å: Chain B: D.224, T.228, D.255, G.275, G.277 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.224, B:T.228, B:D.255, B:G.275, B:G.277 CA.9: 5 residues within 4Å: Chain C: D.224, T.228, D.255, G.275, G.277 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.224, C:T.228, C:D.255, C:G.275, C:G.277 CA.12: 5 residues within 4Å: Chain D: D.224, T.228, D.255, G.275, G.277 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.224, D:T.228, D:D.255, D:G.275, D:G.277

4 x BCZ: 3-(1-ACETYLAMINO-2-ETHYL-BUTYL)-4-GUANIDINO-2-HYDROXY-CYCLOPENTANECARBOXYLIC ACID(Non-covalent)

BCZ.4: 15 residues within 4Å: Chain A: R.47, E.48, L.63, D.80, R.81, R.85, W.108, R.154, E.157, A.176, E.206, E.207, R.223, R.305, Y.340 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:R.154, A:A.176 Hydrogen bonds: A:D.80, A:R.85, A:W.108, A:Y.340 Salt bridges: A:R.47, A:E.48, A:D.80, A:E.157, A:R.223, A:R.305 BCZ.7: 15 residues within 4Å: Chain B: R.47, E.48, L.63, D.80, R.81, R.85, W.108, R.154, E.157, A.176, E.206, E.207, R.223, R.305, Y.340 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:R.154, B:A.176 Hydrogen bonds: B:D.80, B:R.85, B:W.108, B:Y.340 Salt bridges: B:R.47, B:E.48, B:D.80, B:E.157, B:R.223, B:R.305 BCZ.10: 15 residues within 4Å: Chain C: R.47, E.48, L.63, D.80, R.81, R.85, W.108, R.154, E.157, A.176, E.206, E.207, R.223, R.305, Y.340 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:R.154, C:A.176 Hydrogen bonds: C:D.80, C:R.85, C:W.108, C:Y.340 Salt bridges: C:R.47, C:E.48, C:D.80, C:E.157, C:R.223, C:R.305 BCZ.13: 15 residues within 4Å: Chain D: R.47, E.48, L.63, D.80, R.81, R.85, W.108, R.154, E.157, A.176, E.206, E.207, R.223, R.305, Y.340 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:R.154, D:A.176 Hydrogen bonds: D:D.80, D:R.85, D:W.108, D:Y.340 Water bridges: D:E.207, D:E.207 Salt bridges: D:R.47, D:E.48, D:D.80, D:E.157, D:R.223, D:R.305

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oakley, A.J. et al., Structural and Functional Basis of Resistance to Neuraminidase Inhibitors of Influenza B Viruses. J.Med.Chem. (2010)

Release Date

2010-09-01

Peptides

Neuraminidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
M

B
N

C
O

D
P

Neuraminidase

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