SMTL ID : 7zim.1

JC Polyomavirus VP1 in complex with 3'-Sialyllactose glycomacromolecules (aromatic linker)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-pentamer

Ligands

2 x BGC- GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose

BGC-GAL-SIA.1: 9 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 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain C 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, B:S.251 Water bridges: B:S.249, C:F.50 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 Water bridges: C:S.249, C:S.249, C:K.42, C:S.249, D:F.50 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, C:S.251

1 x GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-3)-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 11 PLIP interactions: 9 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:S.43, D:N.106, D:N.247, D:N.247, D:S.249, D:S.251 Water bridges: D:S.43, D:S.43, D:S.249, E:D.48 Hydrophobic interactions: E:F.50

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 5 residues within 4Å: Chain A: V.7, M.84, N.192, L.228, K.230 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.230, A:K.230 PEG.5: 6 residues within 4Å: Chain E: V.65, A.66, R.67, D.173, N.175, Y.235 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:R.67 Water bridges: E:R.67, E:N.175

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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