SMTL ID : 4u60.1

Trichodysplasia spinulosa-associated polyomavirus (TSPyV) VP1 in complex with GM1 oligosaccharide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-pentamer

Ligands

2 x GAL- SIA- NGA: N-acetyl-alpha-neuraminic acid-(2-3)-[2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)]beta-D-galactopyranose(Non-covalent)(Non-functional Binders)

GAL-SIA-NGA.1: 10 residues within 4Å: Chain A: T.50, V.51, A.52, Q.57, D.58, K.59, P.60, T.61 Chain E: H.109, R.114 11 PLIP interactions: 3 interactions with chain E, 8 interactions with chain A Hydrophobic interactions: E:H.109 Hydrogen bonds: E:R.114, E:R.114, A:T.50, A:T.50, A:V.51, A:K.59 Water bridges: A:N.53, A:N.53, A:K.59, A:P.60 GAL-SIA-NGA.2: 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 10 PLIP interactions: 3 interactions with chain B, 7 interactions with chain C Hydrophobic interactions: B:H.109 Hydrogen bonds: B:R.114, B:R.114, C:T.50, C:T.50, C:V.51, C:K.59 Water bridges: C:N.53, C:N.53, C:K.59

2 x BGC- GAL- NGA- GAL- SIA: beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha-neuraminic acid-(2-3)]beta-D-galactopyranose-(1-4)-beta-D-glucopyranose(Non-functional Binders)

BGC-GAL-NGA-GAL-SIA.3: 13 residues within 4Å: Chain C: H.109, R.114, D.118, K.119 Chain D: T.50, V.51, A.52, N.53, Q.57, D.58, K.59, P.60, T.61 10 PLIP interactions: 1 interactions with chain C, 9 interactions with chain D Hydrogen bonds: C:R.114, C:K.119, C:K.119, D:N.53, D:T.50, D:N.53, D:K.59 Water bridges: C:R.114, D:K.48, D:V.51, D:V.51, D:N.53, D:N.53, D:Q.57, C:R.114 Hydrophobic interactions: D:T.61 BGC-GAL-NGA-GAL-SIA.4: 12 residues within 4Å: Chain D: H.109, R.114, D.118, K.119 Chain E: T.50, V.51, A.52, N.53, Q.57, D.58, K.59, T.61 10 PLIP interactions: 2 interactions with chain D, 8 interactions with chain E Hydrogen bonds: D:R.114, D:R.114, D:D.118, D:K.119, E:T.50, E:N.53, E:K.59, E:K.59 Water bridges: E:K.48, E:V.51, E:N.53, E:N.53, E:Q.57, D:R.114, D:R.114

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

GOL.5: 7 residues within 4Å: Chain A: M.77, L.78, N.79, L.82, G.239, D.240 Ligands: GOL.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.78, A:N.79, A:N.79, A:G.239 GOL.6: 5 residues within 4Å: Chain A: N.79, L.87, K.238, G.239 Ligands: GOL.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.239, A:D.240 GOL.8: 7 residues within 4Å: Chain B: N.42, Y.45, L.253, Q.261 Chain C: G.147, N.148, Q.170 8 PLIP interactions: 4 interactions with chain C, 4 interactions with chain B Hydrogen bonds: C:G.147, C:Q.170, B:N.42, B:N.42, B:Q.261, B:Q.261 Water bridges: C:S.55, C:S.55 GOL.9: 7 residues within 4Å: Chain A: N.42, Y.45, M.110 Chain B: S.55, G.147, N.148, Q.170 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.42, A:N.42, B:S.55, B:Q.170 Water bridges: A:A.111, A:A.111, A:Q.261 GOL.12: 5 residues within 4Å: Chain C: N.42, Y.45, L.253, Q.261 Chain D: G.147 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:G.147, C:N.42, C:N.42, C:Q.261 Water bridges: D:S.55, D:Q.170, D:Q.170 GOL.13: 4 residues within 4Å: Chain C: L.87, M.89, K.238, G.239 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.239 Water bridges: C:N.79, C:N.79 GOL.15: 8 residues within 4Å: Chain D: N.42, Y.45, M.110, L.253 Chain E: S.55, G.147, N.148, Q.170 8 PLIP interactions: 5 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:N.42, D:N.42, D:A.111, D:A.111 GOL.16: 4 residues within 4Å: Chain D: M.77, L.78, T.88, K.275 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:T.88, D:T.88, D:K.275, D:K.275 Water bridges: D:L.78 GOL.18: 7 residues within 4Å: Chain A: S.55, G.147, Q.170 Chain E: N.42, Y.45, M.110, L.253 8 PLIP interactions: 4 interactions with chain E, 4 interactions with chain A Hydrogen bonds: E:N.42, A:Q.170 Water bridges: E:A.111, E:A.111, E:Q.261, A:S.55, A:S.55, A:S.55

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

EDO.7: 8 residues within 4Å: Chain A: E.199, N.200, R.202, D.229, V.233, G.234, P.235, L.236 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.202, A:R.202, A:D.229 EDO.10: 8 residues within 4Å: Chain B: E.199, N.200, R.202, D.229, V.233, G.234, P.235, L.236 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.200, B:R.202, B:R.202, B:D.229, B:D.229, B:L.236 EDO.14: 8 residues within 4Å: Chain C: E.199, N.200, R.202, D.229, V.233, G.234, P.235, L.236 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.202, C:R.202, C:D.229 EDO.17: 8 residues within 4Å: Chain D: E.199, N.200, R.202, D.229, V.233, G.234, P.235, L.236 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.202, D:R.202, D:D.229 EDO.19: 8 residues within 4Å: Chain E: E.199, N.200, R.202, D.229, V.233, G.234, P.235, L.236 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:R.202, E:R.202, E:D.229, E:V.233

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

SIA.11: 10 residues within 4Å: Chain A: H.109, R.114 Chain B: T.50, V.51, A.52, Q.57, D.58, K.59, P.60, T.61 9 PLIP interactions: 7 interactions with chain B, 2 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:K.59, B:P.60

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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