SMTL ID : 8agh.1

BK Polyomavirus VP1 mutant E73A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-pentamer

Ligands

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: H.121, F.123, F.192, G.193, T.194 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.193, A:T.194, A:T.194 Water bridges: A:G.193, A:R.255, A:R.255 GOL.3: 4 residues within 4Å: Chain B: H.121, F.192, G.193, T.194 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.194 Water bridges: B:G.193, B:R.255, B:R.255, B:R.255, A:V.207 GOL.5: 5 residues within 4Å: Chain C: H.121, F.123, G.193, T.194, R.255 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:T.194, C:T.194, C:T.194, C:R.255 Water bridges: C:G.193, C:G.193, C:R.255 GOL.7: 6 residues within 4Å: Chain D: H.121, F.123, F.192, G.193, T.194, R.255 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:T.194, D:R.255 Water bridges: D:G.193, D:G.193, D:R.255 GOL.9: 5 residues within 4Å: Chain E: H.121, F.123, F.192, G.193, T.194 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:G.193, E:T.194 Water bridges: E:G.193, E:R.255, E:R.255

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

CL.2: 4 residues within 4Å: Chain A: P.150, K.151, H.164, W.179 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain B: P.150, K.151, D.163, H.164 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain C: P.150, K.151, D.163, H.164 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain D: P.150, K.151, D.163, H.164 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain E: P.150, K.151, H.164 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sorin, M.N. et al., Structural and functional analysis of natural capsid variants suggests sialic acid-independent entry of BK polyomavirus. Cell Rep (2023)

Release Date

2023-02-22

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