SMTL ID : 4u61.1 (1 other biounit)

Trichodysplasia spinulosa-associated polyomavirus (TSPyV) VP1 in complex with 6'-sialyllactose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-pentamer

Ligands

1 x GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose(Non-functional Binders)

GAL-SIA.1: 10 residues within 4Å: Chain A: T.50, V.51, A.52, N.53, Q.57, D.58, K.59, P.60, T.61 Chain E: R.114 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain E Hydrogen bonds: A:T.50, A:T.50, A:V.51, A:K.59, E:R.114, E:R.114 Water bridges: A:N.53, A:N.53, A:K.59

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

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: 2 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:R.114, A:R.114, B:T.50, B:T.50, B:V.51, B:K.59 Water bridges: B:N.53, B:N.53, B:K.59 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: 7 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:T.50, C:T.50, C:V.51, C:K.59, B:R.114, B:R.114 Water bridges: C:N.53, C:N.53, C:K.59 SIA.5: 10 residues within 4Å: Chain D: H.109, R.114 Chain E: T.50, V.51, A.52, Q.57, D.58, K.59, P.60, T.61 7 PLIP interactions: 4 interactions with chain E, 3 interactions with chain D Hydrogen bonds: E:T.50, E:V.51, E:N.53, E:K.59, D:R.114, D:R.114 Hydrophobic interactions: D:H.109

3 x GOL: GLYCEROL(Non-covalent)(Non-functional Binders)

GOL.3: 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: 2 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:Q.170, C:N.42 Water bridges: D:N.148, C:N.42, C:A.111 GOL.6: 8 residues within 4Å: Chain A: S.55, G.147, N.148, Q.170 Chain E: N.42, Y.45, M.110, L.253 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain E Hydrogen bonds: A:S.55, A:S.55, A:Q.170, E:N.42 Water bridges: E:A.111, E:A.111 GOL.7: 5 residues within 4Å: Chain E: H.166, S.168, N.173, H.175, Y.176 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:H.166, E:H.166, E:S.168, E:N.173, E:H.175, E:Y.176

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

Related Entries With Identical Sequence