SMTL ID : 3k36.1 (1 other biounit)

Crystal Structure of B/Perth Neuraminidase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

4 x NAG- NAG- BMA- MAN- MAN- MAN: 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.1: 6 residues within 4Å: Chain A: P.14, R.15, L.16, N.215, R.287, K.350 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.6: 6 residues within 4Å: Chain B: P.14, R.15, L.16, N.215, R.287, K.350 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.11: 6 residues within 4Å: Chain C: P.14, R.15, L.16, N.215, R.287, K.350 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.16: 6 residues within 4Å: Chain D: P.14, R.15, L.16, N.215, R.287, K.350 No protein-ligand interaction detected (PLIP)

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 5 residues within 4Å: Chain A: R.47, D.80, R.223, R.305, Y.340 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.340 Water bridges: A:R.47 Salt bridges: A:R.47, A:R.223, A:R.305 SO4.7: 5 residues within 4Å: Chain B: R.47, D.80, R.223, R.305, Y.340 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.340 Water bridges: B:R.47 Salt bridges: B:R.47, B:R.223, B:R.305 SO4.12: 5 residues within 4Å: Chain C: R.47, D.80, R.223, R.305, Y.340 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Y.340 Water bridges: C:R.47 Salt bridges: C:R.47, C:R.223, C:R.305 SO4.17: 5 residues within 4Å: Chain D: R.47, D.80, R.223, R.305, Y.340 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Y.340 Water bridges: D:R.47 Salt bridges: D:R.47, D:R.223, D:R.305

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

EDO.3: 9 residues within 4Å: Chain A: C.53, G.54, P.55, K.56, E.57, C.58, I.346, K.347 Chain C: E.139 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Water bridges: C:E.139 Hydrogen bonds: A:P.55, A:K.347 EDO.8: 9 residues within 4Å: Chain B: C.53, G.54, P.55, K.56, E.57, C.58, I.346, K.347 Chain D: E.139 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:P.55, B:K.347 Water bridges: D:E.139 EDO.13: 9 residues within 4Å: Chain B: E.139 Chain C: C.53, G.54, P.55, K.56, E.57, C.58, I.346, K.347 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Water bridges: B:E.139 Hydrogen bonds: C:P.55, C:K.347 EDO.18: 9 residues within 4Å: Chain A: E.139 Chain D: C.53, G.54, P.55, K.56, E.57, C.58, I.346, K.347 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain D Water bridges: A:E.139 Hydrogen bonds: D:P.55, D:K.347

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: S.301, K.302, T.303, K.304 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.302, A:T.303, A:T.303, A:K.304, A:K.304 GOL.9: 4 residues within 4Å: Chain B: S.301, K.302, T.303, K.304 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.302, B:T.303, B:T.303, B:K.304, B:K.304 GOL.14: 4 residues within 4Å: Chain C: S.301, K.302, T.303, K.304 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:K.302, C:T.303, C:T.303, C:K.304, C:K.304 GOL.19: 4 residues within 4Å: Chain D: S.301, K.302, T.303, K.304 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:K.302, D:T.303, D:T.303, D:K.304, D:K.304

4 x CA: CALCIUM ION(Non-covalent)

CA.5: 6 residues within 4Å: Chain A: D.224, T.228, D.255, G.275, S.276, G.277 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.224, A:T.228, A:D.255, A:G.275, A:G.277, H2O.4 CA.10: 6 residues within 4Å: Chain B: D.224, T.228, D.255, G.275, S.276, G.277 6 PLIP interactions: 5 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.224, B:T.228, B:D.255, B:G.275, B:G.277, H2O.10 CA.15: 6 residues within 4Å: Chain C: D.224, T.228, D.255, G.275, S.276, G.277 6 PLIP interactions: 5 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.224, C:T.228, C:D.255, C:G.275, C:G.277, H2O.17 CA.20: 6 residues within 4Å: Chain D: D.224, T.228, D.255, G.275, S.276, G.277 6 PLIP interactions: 5 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.224, D:T.228, D:D.255, D:G.275, D:G.277, H2O.23

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
A

B
A

C
A

D
A

Neuraminidase

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