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

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

Coordinates

PDB Format Compare

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: 3 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:H.101 Hydrogen bonds: A:R.106, A:R.106, B:T.42, B:T.42, B:V.43, B:K.51, B:K.51 Water bridges: B:N.45, B:N.45 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 D, 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: D:S.188, C:E.18, 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   PDBe-KB   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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