SMTL ID : 7ziq.1

BK Polyomavirus VP1 in complex with 6'-Sialyllactose glycomacromolecules (aromatic linker)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-pentamer

Ligands

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

BGC-GAL-SIA.1: 9 residues within 4Å: Chain A: L.37, L.42, K.43, N.247, S.249, T.251, Q.253 Chain B: D.49, F.50 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain A Water bridges: B:R.144, B:R.144, B:R.144, B:R.144, A:N.36, A:S.248, A:S.249 Hydrogen bonds: A:K.43, A:N.247, A:S.249 Hydrophobic interactions: B:F.50

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

EDO.2: 2 residues within 4Å: Chain B: G.197, T.198 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.198 Water bridges: B:G.197, B:G.197, B:R.259, B:R.259 EDO.4: 3 residues within 4Å: Chain C: R.268, S.269 Ligands: PEG.5 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.269 EDO.7: 4 residues within 4Å: Chain E: H.125, F.196, G.197, T.198 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:T.198 Water bridges: E:G.197, E:R.259, E:R.259, D:V.211 EDO.8: 7 residues within 4Å: Chain E: E.191, N.192, R.194, D.221, G.226, L.228, K.230 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:R.194, E:R.194, E:D.221, E:K.230, E:K.230

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

SIA.3: 8 residues within 4Å: Chain B: L.37, L.42, K.43, N.247, S.249, T.251, Q.253 Chain C: F.50 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:K.43, B:N.247, B:N.247, B:S.249, B:Q.253 Water bridges: B:S.248, B:S.249 Salt bridges: B:K.43 Hydrophobic interactions: C:F.50 SIA.6: 9 residues within 4Å: Chain D: L.37, L.42, K.43, N.247, S.249, T.251, Q.253 Chain E: D.49, F.50 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:L.37 Hydrogen bonds: D:K.43, D:N.247, D:S.249 Water bridges: D:S.248, D:S.249

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

PEG.5: 1 residues within 4Å: Ligands: EDO.4 No protein-ligand interaction detected (PLIP)

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

Capsid protein VP1: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

C
CCC

D
DDD

E
EEE

Capsid protein VP1

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