SMTL ID : 4u62.1 (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

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: N.42, Y.45, M.110 Chain B: S.55, G.147, N.148, Q.170 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.42, A:N.42, B:Q.170 Water bridges: A:A.111, A:A.111, A:Q.261 GOL.3: 7 residues within 4Å: Chain B: N.42, Y.45, M.110 Chain C: S.55, G.147, N.148, Q.170 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:N.42, C:S.55, C:Q.170 Water bridges: B:A.111, B:A.111, B:A.111 GOL.5: 8 residues within 4Å: Chain A: S.55, G.147, N.148, Q.170 Chain E: N.42, Y.45, M.110, L.253 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:N.42, E:N.42, A:Q.170 Water bridges: E:A.111, E:A.111 GOL.6: 8 residues within 4Å: Chain D: D.41, N.42, Y.45, Q.261 Chain E: G.147, N.148, R.150, Q.170 8 PLIP interactions: 4 interactions with chain E, 4 interactions with chain D Hydrogen bonds: E:G.147, E:R.150, E:R.150, E:Q.170, D:N.42, D:Q.261 Water bridges: D:D.41, D:N.42

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

SIA.2: 11 residues within 4Å: Chain A: H.109, R.114 Chain B: T.50, V.51, A.52, N.53, Q.57, D.58, K.59, P.60, T.61 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:T.50, B:T.50, B:V.51, B:K.59, A:R.114, A:R.114 Water bridges: B:N.53, B:N.53 Hydrophobic interactions: A:H.109 SIA.4: 11 residues within 4Å: Chain B: H.109, R.114 Chain C: T.50, V.51, A.52, N.53, Q.57, D.58, K.59, P.60, T.61 9 PLIP interactions: 6 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:T.50, C:T.50, C:V.51, C:N.53, C:N.53, C:K.59, B:R.114, B:R.114 Hydrophobic interactions: B:H.109

Links

RCSB   PDBe   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
A

B
B

C
C

D
D

E
E

Structural protein VP1

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