SMTL ID : 7b6a.1

BK Polyomavirus VP1 pentamer core (residues 30-299)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.44 Å

Oligo State

homo-pentamer

Ligands

13 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.1: 5 residues within 4Å: Chain A: G.127, E.128, C.225, K.226, S.229 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:G.127, A:K.226, A:S.229, A:S.229, H2O.10 CA.2: 3 residues within 4Å: Chain A: E.19, K.258 Chain B: S.184 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:S.184, A:E.19, H2O.8, H2O.15, H2O.22 CA.3: 2 residues within 4Å: Chain A: T.74, C.75 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.74, H2O.7 CA.4: 4 residues within 4Å: Chain A: S.184, R.185 Chain E: E.19 Ligands: CA.5 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.184, H2O.4, H2O.48, H2O.51 CA.5: 5 residues within 4Å: Chain A: S.184, E.187 Chain E: E.19, K.258 Ligands: CA.4 6 PLIP interactions: 2 interactions with chain A, 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: A:S.184, A:E.187, E:E.19, H2O.6, H2O.51, H2O.55 CA.12: 4 residues within 4Å: Chain B: G.127, E.128, K.226, S.229 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:G.127, B:K.226, B:S.229, B:S.229, H2O.22 CA.13: 1 residues within 4Å: Chain B: T.147 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:T.147, H2O.20, H2O.20, H2O.20, H2O.21 CA.18: 4 residues within 4Å: Chain C: G.127, K.226, S.229, Y.231 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:G.127, C:K.226, C:S.229, C:S.229, H2O.33 CA.19: 2 residues within 4Å: Chain C: T.88, A.211 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:T.88, H2O.27, H2O.30, H2O.32 CA.28: 4 residues within 4Å: Chain D: E.19 Chain E: S.184, R.185, E.187 6 PLIP interactions: 2 interactions with chain E, 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: E:S.184, E:E.187, D:E.19, H2O.42, H2O.50, H2O.55 CA.29: 2 residues within 4Å: Chain D: N.32 Chain E: Y.139 5 PLIP interactions: 1 interactions with chain E, 4 Ligand-Water interactions Metal complexes: E:Y.139, H2O.44, H2O.45, H2O.45, H2O.56 CA.30: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.38: 5 residues within 4Å: Chain E: G.127, E.128, K.226, S.229, Y.231 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:G.127, E:K.226, E:S.229, E:S.229, H2O.57

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

DMS.6: 6 residues within 4Å: Chain A: H.121, F.123, F.192, G.193, T.194 Chain E: H.206 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.194, A:T.194 DMS.7: 5 residues within 4Å: Chain A: L.33, F.241, N.243, Q.249 Chain B: F.46 1 PLIP interactions: 1 interactions with chain B pi-Cation interactions: B:F.46 DMS.14: 8 residues within 4Å: Chain A: H.206 Chain B: H.121, F.123, F.192, G.193, T.194, R.255 Ligands: IOD.16 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.194, A:H.206 DMS.15: 4 residues within 4Å: Chain B: L.33, N.243, Q.249 Chain C: F.46 1 PLIP interactions: 1 interactions with chain C pi-Cation interactions: C:F.46 DMS.20: 9 residues within 4Å: Chain B: H.206 Chain C: H.121, F.122, F.123, F.192, G.193, T.194, R.255 Ligands: IOD.23 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:H.206, C:T.194 DMS.21: 3 residues within 4Å: Chain C: A.62, R.63, N.171 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.63 DMS.22: 5 residues within 4Å: Chain C: L.33, F.241, N.243, Q.249 Chain D: F.46 1 PLIP interactions: 1 interactions with chain D pi-Cation interactions: D:F.46 DMS.31: 6 residues within 4Å: Chain D: L.33, G.102, F.241, N.243, Q.249 Chain E: F.46 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain D pi-Cation interactions: E:F.46, D:F.36 DMS.32: 3 residues within 4Å: Chain D: Y.139, R.140, S.141 1 PLIP interactions: 1 interactions with chain D Water bridges: D:K.142 DMS.33: 6 residues within 4Å: Chain C: H.206 Chain D: H.121, F.123, F.192, G.193, T.194 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.194 DMS.39: 7 residues within 4Å: Chain D: H.206 Chain E: H.121, F.123, F.192, G.193, T.194 Ligands: IOD.41 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:T.194 DMS.40: 5 residues within 4Å: Chain A: F.46 Chain E: L.33, F.241, N.243, Q.249 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:F.46

16 x IOD: IODIDE ION(Non-functional Binders)

IOD.8: 4 residues within 4Å: Chain A: V.90, H.121, L.205, R.255 Ligand excluded by PLIP IOD.9: 4 residues within 4Å: Chain A: K.151, H.164, K.165, W.179 Ligand excluded by PLIP IOD.10: 3 residues within 4Å: Chain A: L.38, K.39, Q.249 Ligand excluded by PLIP IOD.16: 4 residues within 4Å: Chain B: V.90, H.121, R.255 Ligands: DMS.14 Ligand excluded by PLIP IOD.17: 3 residues within 4Å: Chain B: K.151, D.163, H.164 Ligand excluded by PLIP IOD.23: 4 residues within 4Å: Chain C: V.90, H.121, R.255 Ligands: DMS.20 Ligand excluded by PLIP IOD.24: 4 residues within 4Å: Chain C: P.150, K.151, D.163, H.164 Ligand excluded by PLIP IOD.25: 1 residues within 4Å: Chain C: E.19 Ligand excluded by PLIP IOD.26: 3 residues within 4Å: Chain C: L.38, K.39, Q.249 Ligand excluded by PLIP IOD.27: 1 residues within 4Å: Chain C: G.146 Ligand excluded by PLIP IOD.34: 4 residues within 4Å: Chain D: V.90, H.121, L.205, R.255 Ligand excluded by PLIP IOD.35: 4 residues within 4Å: Chain D: P.150, K.151, D.163, H.164 Ligand excluded by PLIP IOD.36: 1 residues within 4Å: Chain D: E.19 Ligand excluded by PLIP IOD.41: 4 residues within 4Å: Chain E: V.90, H.121, R.255 Ligands: DMS.39 Ligand excluded by PLIP IOD.42: 4 residues within 4Å: Chain E: P.150, K.151, D.163, H.164 Ligand excluded by PLIP IOD.43: 2 residues within 4Å: Chain E: V.5, F.21 Ligand excluded by PLIP

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

NA.11: 2 residues within 4Å: Chain A: G.27, N.172 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.172, A:N.172 Water bridges: A:G.27 NA.37: 2 residues within 4Å: Chain D: G.27, N.172 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.27, D:N.172 Water bridges: D:G.27

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: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

C
CCC

D
DDD

E
EEE

Major capsid protein VP1