SMTL ID : 8jpx.1

Cryo-EM structure of PfAgo-guide DNA-target DNA complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

2 x DT- DT- DT- DT- DT- DT: Excess DNA(Non-covalent)

DT-DT-DT-DT-DT-DT.1: 10 residues within 4Å: Chain D: N.402, R.405, K.409, Y.413, F.436, L.437, D.438, F.439, R.440, G.441 Protein-ligand interaction information (PLIP) not available DT-DT-DT-DT-DT-DT.2: 10 residues within 4Å: Chain A: N.402, R.405, K.409, Y.413, F.436, L.437, D.438, F.439, R.440, G.441 Protein-ligand interaction information (PLIP) not available

6 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.558, D.628, H.745 Chain C: T.7 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.558, A:D.628, A:H.745 MG.4: 6 residues within 4Å: Chain A: D.558, V.559, E.596, D.628 Chain C: C.6, T.7 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.558 MG.5: 4 residues within 4Å: Chain A: Q.533, V.770 Chain B: T.1, A.3 No protein-ligand interaction detected (PLIP) MG.6: 4 residues within 4Å: Chain D: D.558, D.628, H.745 Chain F: T.7 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.558, D:D.628, D:H.745 MG.7: 6 residues within 4Å: Chain D: D.558, V.559, E.596, D.628 Chain F: C.6, T.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.558 MG.8: 4 residues within 4Å: Chain D: Q.533, V.770 Chain E: T.1, A.3 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, L. et al., Molecular mechanism for target recognition, dimerization, and activation of Pyrococcus furiosus Argonaute. Mol.Cell (2024)

Release Date

2024-01-31

Peptides

Protein argonaute: AD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

D
A

Protein argonaute