SMTL ID : 7zil.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.24 Å

Oligo State

homo-pentamer

Ligands

3 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 13 PLIP interactions: 11 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, C:S.251 Water bridges: C:S.43, C:S.43, C:S.249, D:F.50 BGC-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: 10 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:S.43, D:N.106, D:N.247, D:N.247, D:S.249, D:S.251, D:S.251 Water bridges: D:S.43, D:S.43, D:S.249 Hydrophobic interactions: E:F.50

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

EDO.4: 3 residues within 4Å: Chain A: V.65, R.67, D.173 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.67 Water bridges: A:N.175 EDO.5: 3 residues within 4Å: Chain A: F.127, F.196, T.217 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.217 EDO.6: 3 residues within 4Å: Chain A: P.69, L.70, P.71 1 PLIP interactions: 1 interactions with chain A Water bridges: A:L.70 EDO.10: 3 residues within 4Å: Chain B: V.65, R.67, D.173 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:V.65, B:D.173 Water bridges: B:R.67, B:N.175, B:Y.235 EDO.16: 5 residues within 4Å: Chain D: H.125, F.127, F.196, G.197, T.198 2 PLIP interactions: 2 interactions with chain D Water bridges: D:G.197, D:G.197 EDO.20: 3 residues within 4Å: Chain E: P.69, L.70, P.71 No protein-ligand interaction detected (PLIP) EDO.21: 4 residues within 4Å: Chain E: S.47, D.48, S.52, S.54 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:D.48, E:S.52, E:S.54 Water bridges: E:D.48, E:D.48, E:S.54, E:S.54

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

CL.7: 3 residues within 4Å: Chain A: K.42, S.43, Q.253 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain B: R.248, S.249 Ligand excluded by PLIP CL.22: 2 residues within 4Å: Chain E: K.42, S.43 Ligand excluded by PLIP

10 x NA: SODIUM ION(Non-functional Binders)

NA.8: 2 residues within 4Å: Chain A: M.101 Chain B: E.181 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.181, A:M.101 NA.9: 4 residues within 4Å: Chain A: P.154, K.155, E.167, H.168 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.155, A:E.167 NA.12: 2 residues within 4Å: Chain B: M.101 Chain C: E.181 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.181 Water bridges: C:E.181 NA.13: 4 residues within 4Å: Chain B: P.154, K.155, E.167, H.168 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.155, B:E.167, B:H.168 NA.14: 2 residues within 4Å: Chain C: M.101 Chain D: E.181 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:M.101 NA.15: 4 residues within 4Å: Chain C: P.154, K.155, E.167, H.168 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.155, C:E.167, C:H.168 NA.17: 3 residues within 4Å: Chain D: M.101 Chain E: E.181, W.254 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:M.101 NA.18: 3 residues within 4Å: Chain D: P.154, K.155, H.168 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.155, D:K.155, D:H.168 NA.23: 2 residues within 4Å: Chain A: E.181 Chain E: M.101 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:M.101, A:E.181 NA.24: 4 residues within 4Å: Chain E: P.154, K.155, E.167, H.168 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:K.155, E:K.155

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

PEG.19: 6 residues within 4Å: Chain E: V.65, A.66, R.67, D.173, N.175, Y.235 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:R.67, E:R.67, E:N.175, E:Y.235, E:Y.235 Water bridges: 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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