SMTL ID : 6esb.1 (3 other biounits)

BK polyomavirus + 20 mM GT1b oligosaccharide

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-mer

Ligands

6 x SIA- SIA: N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-alpha-neuraminic acid(Non-covalent)(Post Translational Modification)

SIA-SIA.1: 11 residues within 4Å: Chain A: L.62, F.65, L.67, K.68, F.270, N.272, S.274, T.276, Q.278 Chain B: F.75 Chain E: H.138 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.65, A:F.270, B:F.75 Hydrogen bonds: A:K.68, A:N.272, A:N.272, A:S.274, A:Q.278 SIA-SIA.2: 11 residues within 4Å: Chain A: H.138 Chain B: L.62, F.65, L.67, K.68, F.270, N.272, S.274, T.276, Q.278 Chain C: F.75 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:F.65, B:F.270, C:F.75 Hydrogen bonds: B:K.68, B:N.272, B:N.272, B:S.274, B:Q.278 SIA-SIA.3: 11 residues within 4Å: Chain B: H.138 Chain C: L.62, F.65, L.67, K.68, F.270, N.272, S.274, T.276, Q.278 Chain D: F.75 11 PLIP interactions: 1 interactions with chain D, 10 interactions with chain C Hydrophobic interactions: D:F.75, C:F.65, C:F.270 Hydrogen bonds: C:K.68, C:N.272, C:N.272, C:S.274, C:S.274, C:T.276, C:T.276, C:Q.278 SIA-SIA.4: 11 residues within 4Å: Chain C: H.138 Chain D: L.62, F.65, L.67, K.68, F.270, N.272, S.274, T.276, Q.278 Chain E: F.75 12 PLIP interactions: 11 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: D:L.62, D:F.65, D:F.270, E:F.75 Hydrogen bonds: D:K.68, D:N.272, D:N.272, D:S.274, D:T.276, D:T.276, D:Q.278 Salt bridges: D:K.68 SIA-SIA.5: 11 residues within 4Å: Chain A: F.75 Chain D: H.138 Chain E: L.62, F.65, L.67, K.68, F.270, N.272, S.274, T.276, Q.278 11 PLIP interactions: 1 interactions with chain A, 10 interactions with chain E Hydrophobic interactions: A:F.75, E:L.62, E:F.65, E:F.270 Hydrogen bonds: E:K.68, E:N.272, E:N.272, E:S.274, E:S.274, E:T.276, E:Q.278 SIA-SIA.6: 9 residues within 4Å: Chain F: L.62, F.65, L.67, K.68, F.270, N.272, S.274, T.276, Q.278 10 PLIP interactions: 10 interactions with chain F Hydrophobic interactions: F:L.62, F:F.65, F:F.270 Hydrogen bonds: F:K.68, F:N.272, F:N.272, F:T.276, F:T.276, F:Q.278 Salt bridges: F:K.68

6 x CA: CALCIUM ION(Non-covalent)

CA.7: 3 residues within 4Å: Chain A: S.213, E.216 Chain E: E.48 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain E Metal complexes: A:S.213, A:E.216, E:E.48, E:E.48 CA.8: 3 residues within 4Å: Chain A: E.48 Chain B: S.213, E.216 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Metal complexes: B:S.213, B:E.216, A:E.48, A:E.48 CA.9: 4 residues within 4Å: Chain B: E.48 Chain C: S.213, E.216 Chain F: E.330 5 PLIP interactions: 1 interactions with chain F, 2 interactions with chain C, 2 interactions with chain B Metal complexes: F:E.330, C:S.213, C:E.216, B:E.48, B:E.48 CA.10: 3 residues within 4Å: Chain C: E.48 Chain D: S.213, E.216 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Metal complexes: D:S.213, D:E.216, C:E.48 CA.11: 3 residues within 4Å: Chain C: E.330 Chain F: S.213, E.216 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:S.213, F:E.216 CA.12: 3 residues within 4Å: Chain D: E.48 Chain E: S.213, E.216 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain E Metal complexes: D:E.48, D:E.48, E:S.213

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hurdiss, D.L. et al., The Structure of an Infectious Human Polyomavirus and Its Interactions with Cellular Receptors. Structure (2018)

Release Date

2018-05-02

Peptides

Capsid protein VP1: ABCDEF
Minor capsid protein VP2: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

B
2

C
3

D
4

E
5

F
6

G
7

Capsid protein VP1

Minor capsid protein VP2

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