SMTL ID : 7zin.1

JC Polyomavirus VP1 in complex with 6'-Sialyllactose glycomacromolecules (aliphatic linker)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-pentamer

Ligands

2 x BGC- GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose

BGC-GAL-SIA.1: 10 residues within 4Å: Chain B: L.37, K.42, S.43, N.106, N.247, S.249, S.251, Q.253 Chain C: F.50, E.51 12 PLIP interactions: 2 interactions with chain C, 10 interactions with chain B Water bridges: C:E.51, B:S.43, B:S.43, B:S.249, C:F.50 Hydrophobic interactions: B:L.37, C:F.50 Hydrogen bonds: B:S.43, B:N.106, B:N.247, B:N.247, B:S.249, B:S.251 BGC-GAL-SIA.2: 9 residues within 4Å: Chain C: L.37, K.42, S.43, N.106, N.247, S.249, S.251, Q.253 Chain D: F.50 12 PLIP interactions: 10 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:L.37, D:F.50 Hydrogen bonds: C:S.43, C:N.106, C:N.247, C:N.247, C:S.249, C:S.251 Water bridges: C:K.42, C:N.106, C:S.249, D:F.50

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

GAL-SIA.3: 9 residues within 4Å: Chain D: L.37, K.42, S.43, N.106, N.247, S.249, S.251, Q.253 Chain E: F.50 9 PLIP interactions: 8 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: D:L.37, E:F.50 Hydrogen bonds: D:S.43, D:N.106, D:N.247, D:N.247, D:S.249, D:S.251 Water bridges: D:S.249

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

EDO.4: 5 residues within 4Å: Chain A: H.125, F.127, F.196, G.197, T.198 2 PLIP interactions: 2 interactions with chain A Water bridges: A:G.197, A:G.197 EDO.5: 3 residues within 4Å: Chain B: V.65, R.67, D.173 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.67, B:N.175 EDO.6: 3 residues within 4Å: Chain B: H.125, G.197, T.198 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Water bridges: B:G.197, B:R.259, A:I.211 EDO.7: 4 residues within 4Å: Chain C: H.125, F.127, G.197, T.198 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:H.125 Water bridges: C:G.197, C:R.259, B:I.211 EDO.8: 3 residues within 4Å: Chain D: H.125, G.197, T.198 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:H.125 Water bridges: D:G.197, D:G.197, D:R.259 EDO.9: 2 residues within 4Å: Chain E: F.196, T.217 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:T.217 EDO.10: 2 residues within 4Å: Chain E: L.70, P.71 No protein-ligand interaction detected (PLIP) EDO.11: 4 residues within 4Å: Chain E: N.81, I.82, L.83, R.269 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:I.82

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Konietzny, P.B. et al., Synthesis of Homo- and Heteromultivalent Fucosylated and Sialylated Oligosaccharide Conjugates via Preactivated N -Methyloxyamine Precision Macromolecules and Their Binding to Polyomavirus Capsid Proteins. Biomacromolecules (2022)

Release Date

2022-12-21

Peptides

Major capsid protein VP1: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

C
CCC

D
DDD

E
EEE

Major capsid protein VP1

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