SMTL ID : 6y6a.6 (7 other biounits)

Structure of Finch Polyomavirus VP1 in complex with 2-O-Methyl-5-N-acetyl-alpha-D-neuraminic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

homo-pentamer

Ligands

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

SIA.1: 11 residues within 4Å: Chain A: T.41, V.42, A.43, S.44, N.48, D.49, A.50, P.51, H.52 Chain E: H.100, R.105 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain E Hydrophobic interactions: A:A.43 Hydrogen bonds: A:T.41, A:T.41, A:V.42, A:S.44, A:A.50, E:R.105, E:R.105 Salt bridges: A:H.52 SIA.4: 9 residues within 4Å: Chain A: R.105 Chain B: T.41, V.42, A.43, N.48, D.49, A.50, P.51, H.52 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:A.43 Hydrogen bonds: B:T.41, B:T.41, B:V.42, B:A.50, A:R.105 Salt bridges: B:H.52 SIA.5: 9 residues within 4Å: Chain B: R.105 Chain C: T.41, V.42, A.43, N.48, D.49, A.50, P.51, H.52 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:A.43 Hydrogen bonds: C:T.41, C:T.41, C:V.42, C:A.50, B:R.105 Salt bridges: C:H.52 SIA.6: 11 residues within 4Å: Chain C: H.100, R.105 Chain D: T.41, V.42, A.43, S.44, N.48, D.49, A.50, P.51, H.52 9 PLIP interactions: 7 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:A.43 Hydrogen bonds: D:T.41, D:T.41, D:V.42, D:S.44, D:A.50, C:R.105, C:R.105 Salt bridges: D:H.52 SIA.8: 9 residues within 4Å: Chain D: R.105 Chain E: T.41, V.42, A.43, N.48, D.49, A.50, P.51, H.52 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:A.43 Hydrogen bonds: E:T.41, E:S.44, E:A.50 Salt bridges: E:H.52

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

CL.2: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.3: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.7: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.9: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.10: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stroh, L.J. et al., Structural Basis and Evolution of Glycan Receptor Specificities within the Polyomavirus Family. Mbio (2020)

Release Date

2020-07-08

Peptides

Capsid protein VP1: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
Z

B
a

C
b

D
c

E
d

Capsid protein VP1

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