SMTL ID : 8hf1.1

DmDcr-2/R2D2/LoqsPD with 19bp-dsRNA in Trimer state

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-3-mer

Ligands

3 x G- A- G- A- C- U- U- G- G: RNA (5'-R(P*GP*AP*GP*AP*CP*UP*UP*GP*G)-3')(Non-covalent)

G-A-G-A-C-U-U-G-G.1: 23 residues within 4Å: Chain A: T.144, G.145, H.146, H.147, P.148, K.176, G.177, N.178, R.259, K.482, L.571, H.575, Q.579 Chain G: C.1, C.2, A.3, A.4, G.5, U.6, C.7, U.8, C.9, U.10 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:V.66, A:G.89, A:K.262, A:Q.278, A:Q.278, A:R.394, A:R.426, A:R.426, A:S.460, A:S.461, A:S.461, A:E.465, A:R.576 Salt bridges: A:R.268, A:R.268, A:R.394, A:R.426, A:R.576 G-A-G-A-C-U-U-G-G.2: 25 residues within 4Å: Chain D: T.144, G.145, H.146, H.147, P.148, K.176, G.177, N.178, E.179, Q.312, L.571, H.575, F.588, I.590, K.641 Chain I: C.1, C.2, A.3, A.4, G.5, U.6, C.7, U.8, C.9, U.10 Protein-ligand interaction information (PLIP) not available G-A-G-A-C-U-U-G-G.3: 19 residues within 4Å: Chain F: T.144, H.146, H.147, K.176, G.177, N.178, R.259, K.262, K.641 Chain J: C.1, C.2, A.3, A.4, G.5, U.6, C.7, U.8, C.9, U.10 Protein-ligand interaction information (PLIP) not available

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Deng, T. et al., Structural mechanism of R2D2 and Loqs-PD synergistic modulation on DmDcr-2 oligomers. Nat Commun (2023)

Release Date

2023-09-06

Peptides

Dicer-2, isoform A: ADF
Loquacious, isoform D: B
LD06392p: CEH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

F
G

B
B

C
C

E
F

H
I

Dicer-2, isoform A

Loquacious, isoform D

LD06392p