SMTL ID : 8yii.1

DmDcr-2/LoqsPD/slm2 in dicing state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

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

ADP.1: 15 residues within 4Å: Chain A: K.6, P.7, R.8, Q.11, P.28, T.29, G.30, S.31, G.32, K.33, T.34, F.35, Y.213, D.468 Ligands: MG.4 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:K.6, A:K.6, A:R.8, A:R.8, A:Q.11, A:G.30, A:S.31, A:G.32, A:K.33, A:T.34 Salt bridges: A:K.33 pi-Stacking: A:F.35, A:F.35

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: E.1212, K.1363, D.1367, E.1370 Chain C: U.84 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.1212, A:D.1367, A:E.1370, A:E.1370 MG.3: 5 residues within 4Å: Chain A: E.1471, D.1613, E.1616 Chain C: A.22, G.23 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.1471, A:D.1613, A:E.1616, A:E.1616 MG.4: 2 residues within 4Å: Chain A: T.34 Ligands: ADP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.34 MG.5: 3 residues within 4Å: Chain A: E.1209, E.1212 Chain C: C.85 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.1209, A:E.1212 MG.6: 3 residues within 4Å: Chain A: Q.1468, E.1471 Chain C: G.24 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.1471

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cao, N. et al., Structural basis of endo-siRNA processing by Drosophila Dicer-2 and Loqs-PD. Nucleic Acids Res. (2025)

Release Date

2025-03-05

Peptides

Dicer-2, isoform A: A
Isoform PD of Protein Loquacious: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dicer-2, isoform A

Isoform PD of Protein Loquacious

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