SMTL ID : 7pds.1

The structure of PriRep1 with dsDNA

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

1 x DT- DA- DA- DA- DA: polyA(Non-covalent)

DT-DA-DA-DA-DA.1: 17 residues within 4Å: Chain A: S.250, Y.251 Chain B: R.248, S.250, Y.251, G.252 Chain C: R.248, A.249, S.250, Y.251, G.252 Chain D: R.248, S.250, Y.251 Chain E: R.248, S.250, Y.251 Protein-ligand interaction information (PLIP) not available

6 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Non-covalent)

AGS.2: 19 residues within 4Å: Chain A: G.181, Q.182, G.183, V.184, G.185, K.186, S.187, T.188, E.223, E.224, F.298 Chain B: K.171, D.173, R.281, R.282, D.323, K.324, L.327 Ligands: MG.3 17 PLIP interactions: 10 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:G.183, A:V.184, A:G.185, A:K.186, A:K.186, A:S.187, A:T.188, A:T.188, A:E.224, B:R.281, B:R.282, B:R.282, B:D.323 Salt bridges: A:K.186, B:K.171, B:R.281, B:R.281 AGS.4: 18 residues within 4Å: Chain B: G.181, Q.182, G.183, V.184, G.185, K.186, S.187, T.188, E.224, F.298 Chain C: K.171, D.173, R.281, R.282, D.323, K.324, L.327 Ligands: MG.5 14 PLIP interactions: 7 interactions with chain C, 7 interactions with chain B Hydrogen bonds: C:R.281, C:R.282, C:R.282, C:D.323, B:G.185, B:K.186, B:S.187, B:T.188, B:T.188 Salt bridges: C:K.171, C:R.281, C:R.281, B:K.186 pi-Stacking: B:F.298 AGS.6: 22 residues within 4Å: Chain C: G.181, Q.182, G.183, V.184, G.185, K.186, S.187, T.188, E.224, T.267, K.290, F.298, D.299 Chain D: K.171, D.173, K.237, R.281, R.282, D.323, K.324, L.327 Ligands: MG.7 22 PLIP interactions: 11 interactions with chain C, 11 interactions with chain D Hydrogen bonds: C:G.181, C:G.183, C:V.184, C:G.185, C:K.186, C:K.186, C:S.187, C:T.188, C:E.224, C:K.290, D:K.171, D:D.173, D:K.237, D:K.237, D:R.281, D:R.282, D:R.282, D:D.323, D:K.324 Salt bridges: C:K.186, D:K.171, D:R.281 AGS.8: 15 residues within 4Å: Chain D: G.181, Q.182, G.185, K.186, S.187, T.188, E.224, F.298 Chain E: K.171, R.281, R.282, D.323, K.324, L.327 Ligands: MG.9 13 PLIP interactions: 6 interactions with chain E, 7 interactions with chain D Hydrogen bonds: E:R.282, E:R.282, E:D.323, D:G.185, D:K.186, D:K.186, D:S.187, D:T.188, D:T.188 Salt bridges: E:K.171, E:R.281, E:R.281, D:K.186 AGS.10: 11 residues within 4Å: Chain E: Q.182, G.183, V.184, G.185, K.186, S.187, T.188, F.298 Chain F: R.281, K.330, S.333 15 PLIP interactions: 12 interactions with chain E, 3 interactions with chain F Hydrogen bonds: E:Q.182, E:Q.182, E:G.185, E:K.186, E:K.186, E:S.187, E:S.187, E:S.187, E:T.188, F:S.333, F:S.333 Salt bridges: E:K.186, F:R.281 pi-Stacking: E:F.298, E:F.298 AGS.11: 10 residues within 4Å: Chain F: G.181, Q.182, G.183, V.184, G.185, K.186, S.187, T.188, E.223, F.298 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:Q.182, F:Q.182, F:G.185, F:K.186, F:K.186, F:S.187, F:T.188, F:E.223 Salt bridges: F:K.186 pi-Stacking: F:F.298, F:F.298

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: S.187, E.223 Ligands: AGS.2 No protein-ligand interaction detected (PLIP) MG.5: 4 residues within 4Å: Chain B: S.187, E.224, T.267 Ligands: AGS.4 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain C: S.187 Chain D: R.282 Ligands: AGS.6 No protein-ligand interaction detected (PLIP) MG.9: 3 residues within 4Å: Chain D: S.187, E.224 Ligands: AGS.8 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Qiao, C. et al., Staphylococcal self-loading helicases couple the staircase mechanism with inter domain high flexibility. Nucleic Acids Res. (2022)

Release Date

2022-07-13

Peptides

Similar to D. nodosus vapE: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Similar to D. nodosus vapE