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

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

Coordinates

PDB Format

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)(Non-functional Binders)

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: 2 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:R.106, A:R.106, B:T.42, B:T.42, B:V.43, B:K.51 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-covalent)

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: 2 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:N.34, D:S.47, D:Q.162, D:Q.162 Water bridges: C:Q.253, D:N.140

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

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   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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