SMTL ID : 7b6c.2 (1 other biounit)

BK Polyomavirus VP1 pentamer fusion with long C-terminal extended arm

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.48 Å

Oligo State

homo-pentamer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 3 residues within 4Å: Chain A: E.17, E.32 Chain B: S.197 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Metal complexes: B:S.197, A:E.32 CA.3: 5 residues within 4Å: Chain D: E.17, R.19, E.32 Chain E: S.197, E.200 4 PLIP interactions: 2 interactions with chain E, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: E:S.197, E:E.200, D:E.32, H2O.11

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.2: 4 residues within 4Å: Chain C: H.134, F.136, F.205, R.268 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.268

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Osipov, E.M. et al., Discovery of novel druggable pockets on polyomavirus VP1 through crystallographic fragment-based screening to develop capsid assembly inhibitors. Rsc Chem Biol (2022)

Release Date

2022-06-22

Peptides

Major capsid protein VP1,Major capsid protein VP1: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
FFF

B
GGG

C
HHH

D
III

E
JJJ

Major capsid protein VP1,Major capsid protein VP1

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