SMTL ID : 4u62.2 (1 other biounit)

Trichodysplasia spinulosa-associated polyomavirus (TSPyV) VP1 in complex with 3'-sialyllactose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-pentamer

Ligands

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

EDO.1: 6 residues within 4Å: Chain B: N.42, Y.45 Chain C: S.55, G.147, N.148, Q.170 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:N.42, C:S.55, C:S.55, C:Q.170 Water bridges: B:A.111

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain C: N.42, Y.45, M.110 Chain D: S.55, G.147, N.148, Q.170 5 PLIP interactions: 1 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:Q.170, C:N.42 Water bridges: C:A.111, C:A.111, C:Q.261 GOL.3: 7 residues within 4Å: Chain D: N.42, Y.45, M.110 Chain E: S.55, G.147, N.148, Q.170 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain E Hydrogen bonds: D:N.42, E:S.55, E:S.55, E:Q.170 Water bridges: D:A.111, D:A.111 GOL.4: 8 residues within 4Å: Chain A: G.147, N.148, R.150, Q.170 Chain E: N.42, Y.45, L.253, Q.261 9 PLIP interactions: 3 interactions with chain E, 6 interactions with chain A Hydrogen bonds: E:N.42, E:Q.261, E:Q.261, A:G.147, A:R.150, A:Q.170, A:Q.170 Water bridges: A:R.150, A:R.150

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

SIA.5: 11 residues within 4Å: Chain D: H.109, R.114 Chain E: T.50, V.51, A.52, N.53, Q.57, D.58, K.59, P.60, T.61 8 PLIP interactions: 3 interactions with chain D, 5 interactions with chain E Hydrophobic interactions: D:H.109 Hydrogen bonds: D:R.114, D:R.114, E:T.50, E:T.50, E:V.51, E:N.53, E:K.59

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stroh, L.J. et al., Trichodysplasia spinulosa-Associated Polyomavirus Uses a Displaced Binding Site on VP1 to Engage Sialylated Glycolipids. Plos Pathog. (2015)

Release Date

2015-08-05

Peptides

Structural protein VP1: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
G

C
H

D
I

E
J

Structural protein VP1

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