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

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-pentamer

Ligands

5 x GXB: Sialylated precision glycomacromolecule(Non-covalent)

GXB.1: 9 residues within 4Å: Chain A: T.42, V.43, A.44, Q.49, D.50, K.51, P.52, T.53 Chain E: H.101 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:T.42, A:K.51, A:K.51 Water bridges: A:V.43, A:N.45, E:R.106 GXB.2: 11 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, P.52, T.53 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:T.42, B:T.42, B:V.43, B:K.51, B:K.51, A:R.106, A:R.106 Water bridges: B:N.45, B:N.45 Hydrophobic interactions: A:H.101 GXB.3: 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 9 PLIP interactions: 7 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:T.42, C:T.42, C:V.43, C:K.51, C:K.51, B:R.106, B:R.106 Water bridges: C:N.45, C:N.45 GXB.6: 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: 6 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:T.42, D:T.42, D:V.43, D:K.51, D:K.51, C:R.106, C:R.106 Water bridges: D:N.45 Hydrophobic interactions: C:H.101 GXB.7: 11 residues within 4Å: Chain D: H.101, R.106 Chain E: T.42, V.43, A.44, Q.49, D.50, K.51, P.52, T.53 Ligands: GOL.8 9 PLIP interactions: 6 interactions with chain E, 3 interactions with chain D Hydrogen bonds: E:T.42, E:T.42, E:V.43, E:N.45, E:K.51, E:K.51, D:R.106, D:R.106 Hydrophobic interactions: D:H.101

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 2 residues within 4Å: Chain C: E.18 Chain D: S.188 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: C:E.18, D:S.188, H2O.28, H2O.37, H2O.40

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 3 residues within 4Å: Chain C: L.70, T.80, K.267 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 3 residues within 4Å: Chain E: N.45, Q.49 Ligands: GXB.7 3 PLIP interactions: 3 interactions with chain E Water bridges: E:N.45, E:Q.49, E:Q.49

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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