SMTL ID : 7zio.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 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: 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: 2 interactions with chain C, 9 interactions with chain B Water bridges: C:F.50, 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: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:S.249, C:S.251, 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: 7 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.249, E:R.144 Hydrophobic interactions: E:F.50

9 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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.125, A:T.198 Water bridges: A:G.197, A:G.197 EDO.5: 2 residues within 4Å: Chain A: M.84, K.230 No protein-ligand interaction detected (PLIP) EDO.6: 4 residues within 4Å: Chain B: H.125, F.127, G.197, T.198 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.125 Water bridges: B:G.197, B:G.197, B:R.259 EDO.7: 6 residues within 4Å: Chain B: N.74, L.83, M.84, K.230, G.231, D.232 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.74, B:L.83, B:G.231 EDO.8: 4 residues within 4Å: Chain C: H.125, F.196, G.197, T.198 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain C Water bridges: B:I.211, C:G.197, C:R.259 Hydrogen bonds: C:H.125 EDO.9: 6 residues within 4Å: Chain D: H.125, F.127, F.196, G.197, T.198 Ligands: EDO.12 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Water bridges: C:I.211, D:G.197, D:R.259 EDO.11: 4 residues within 4Å: Chain D: G.31, D.32, P.33, D.58 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.31 EDO.12: 7 residues within 4Å: Chain D: V.94, H.125, V.208, L.209, H.210, R.259 Ligands: EDO.9 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:H.210, D:H.210, D:R.259 Water bridges: D:R.259 EDO.13: 4 residues within 4Å: Chain E: H.125, F.127, G.197, T.198 2 PLIP interactions: 2 interactions with chain E Water bridges: E:G.197, E:G.197

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 8 residues within 4Å: Chain C: H.104 Chain D: S.45, S.47, S.52, D.53, S.54, P.55, M.59 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.52, D:S.54 Water bridges: D:I.46, D:N.56

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

PEG.14: 7 residues within 4Å: Chain E: F.25, L.26, T.27, E.29, S.64, V.65, N.175 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:T.27, E:E.29, E:N.175 Water bridges: E:K.176

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

CL.15: 2 residues within 4Å: Chain E: L.83, R.269 Ligand excluded by 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

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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