SMTL ID : 6hku.1 (1 other biounit)

Trichodysplasia spinulosa-associated polyomavirus (TSPyV) VP1 in complex with sialylated precision glycooligomers

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

homo-pentamer

Ligands

2 x GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose(Non-covalent)

GAL-SIA.1: 10 residues within 4Å: Chain A: H.101, R.106 Chain B: T.42, V.43, A.44, N.45, Q.49, D.50, K.51, T.53 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:T.42, B:T.42, B:V.43, B:K.51, A:R.106, A:R.106 Water bridges: B:N.45, B:N.45 GAL-SIA.2: 11 residues within 4Å: Chain B: H.101, R.106 Chain C: T.42, V.43, A.44, N.45, Q.49, D.50, K.51, P.52, T.53 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:T.42, C:T.42, C:V.43, C:N.45, C:K.51, B:R.106, B:R.106 Water bridges: C:N.45

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain C: N.34, Y.37, M.102, L.245 Chain D: S.47, G.139, N.140, Q.162 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:S.47, D:Q.162, D:Q.162, C:N.34 Water bridges: D:N.140, C:Q.253

1 x SIA: N-acetyl-alpha-neuraminic acid(Non-covalent)

SIA.4: 11 residues within 4Å: Chain C: H.101, R.106 Chain D: T.42, V.43, A.44, N.45, Q.49, D.50, K.51, P.52, T.53 9 PLIP interactions: 7 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:A.44 Hydrogen bonds: D:T.42, D:T.42, D:V.43, D:N.45, D:K.51, C:R.106, C:R.106 Water bridges: D:N.45

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Baier, M. et al., Divalent Sialylated Precision Glycooligomers Binding to Polyomaviruses and the Effect of Different Linkers. Macromol Biosci (2019)

Release Date

2019-03-27

Peptides

Capsid protein VP1: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Capsid protein VP1

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