SMTL ID : 7lar.1

Cryo-EM structure of PCV2 Replicase bound to ssDNA

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

1 x DT- DT- DT- DT- DT- DT: DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3')(Non-covalent)

DT-DT-DT-DT-DT-DT.1: 23 residues within 4Å: Chain A: W.202, E.238, K.240, G.241 Chain B: W.202, T.239, K.240, G.241 Chain C: W.202, K.240, G.241 Chain D: W.202, E.238, T.239, K.240, G.241 Chain E: W.202, T.239, K.240, G.241 Chain F: W.202, K.240, G.241 Protein-ligand interaction information (PLIP) not available

4 x ADP: ADENOSINE-5'-DIPHOSPHATE(Covalent)(Non-covalent)

ADP.2: 16 residues within 4Å: Chain A: P.176, G.177, C.178, G.179, K.180, S.181, K.182, D.215, D.216, N.256 Chain B: D.231, R.232, Y.233, R.276, R.277 Ligands: MG.3 11 PLIP interactions: 5 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:R.277, A:G.177, A:G.179, A:S.181, A:S.181 Salt bridges: B:R.276, B:R.276, B:R.277, A:K.180, A:K.180 pi-Cation interactions: B:R.232 ADP.4: 12 residues within 4Å: Chain B: P.176, G.177, G.179, K.180, S.181, K.182 Chain C: D.231, R.232, Y.233, R.276, R.277 Ligands: MG.5 12 PLIP interactions: 8 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:G.177, B:G.179, B:K.180, B:S.181, B:S.181, B:K.182, C:D.231, C:Y.233 Salt bridges: B:K.180, C:R.276, C:R.276 pi-Cation interactions: B:K.182 ADP.6: 12 residues within 4Å: Chain C: P.176, G.177, C.178, G.179, K.180, S.181, K.182 Chain D: D.231, R.232, Y.233, R.277 Ligands: MG.7 11 PLIP interactions: 7 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:G.177, C:G.179, C:K.180, C:S.181, C:K.182, D:D.231, D:R.232, D:R.277 Salt bridges: C:K.180 pi-Cation interactions: C:K.182, D:R.232 ADP.8: 11 residues within 4Å: Chain D: G.177, C.178, G.179, K.180, S.181, K.182 Chain E: R.232, Y.233, R.276, R.277 Ligands: MG.9 12 PLIP interactions: 8 interactions with chain D, 4 interactions with chain E Hydrogen bonds: D:G.177, D:G.179, D:G.179, D:K.180, D:S.181, D:K.182, D:K.182, E:Y.233, E:R.277 Salt bridges: D:K.180, E:R.232 pi-Cation interactions: E:R.232

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: K.180, D.215, D.216, N.256 Chain B: R.277 Ligands: ADP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.216 MG.5: 6 residues within 4Å: Chain B: S.181, D.215, D.216 Chain C: D.231, Y.233 Ligands: ADP.4 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:S.181, B:D.215 MG.7: 5 residues within 4Å: Chain C: K.180, S.181, D.215, D.216 Ligands: ADP.6 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:S.181, C:D.215, C:D.216 MG.9: 6 residues within 4Å: Chain D: K.180, S.181, D.215, D.216 Chain E: D.231 Ligands: ADP.8 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:S.181

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tarasova, E. et al., Mechanism of DNA Interaction and Translocation by the Replicase of a Circular Rep-Encoding Single-Stranded DNA Virus. Mbio (2021)

Release Date

2021-08-25

Peptides

ATP-dependent helicase Rep: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

ATP-dependent helicase Rep

Related Entries With Identical Sequence