SMTL ID : 8dg5.1

Structural Basis of MicroRNA Biogenesis by Dicer-1 and Its Partner Protein Loqs-PB - complex IIb

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

11 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.1: 5 residues within 4Å: Chain A: D.1749, L.1752, V.1780, E.1908 Chain B: A.37 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.1749, A:E.1908 MG.2: 2 residues within 4Å: Chain A: A.1199 Chain B: A.2 No protein-ligand interaction detected (PLIP) MG.3: 3 residues within 4Å: Chain A: N.1210 Chain B: A.9, G.10 No protein-ligand interaction detected (PLIP) MG.5: 5 residues within 4Å: Chain A: E.1745, K.1901, D.1905, E.1908 Chain B: C.38 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.1905, A:E.1908 MG.6: 1 residues within 4Å: Chain B: A.40 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain A: R.2225 Chain B: U.20, A.21 No protein-ligand interaction detected (PLIP) MG.8: 1 residues within 4Å: Chain B: A.9 No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain B: G.10, G.11 No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Chain B: U.41, C.43 No protein-ligand interaction detected (PLIP) MG.11: 1 residues within 4Å: Chain B: C.38 No protein-ligand interaction detected (PLIP) MG.12: 2 residues within 4Å: Chain B: G.1, A.2 No protein-ligand interaction detected (PLIP)

1 x U5P: URIDINE-5'-MONOPHOSPHATE(Non-covalent)

U5P.4: 11 residues within 4Å: Chain A: R.994, R.996, R.1027, D.1195, H.1196, T.1197, S.1198, A.1199, R.1200, R.1207 Chain B: G.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:R.994, A:D.1195 Hydrogen bonds: A:R.994, A:R.1027, A:H.1196, A:A.1199, A:R.1200 Salt bridges: A:R.1200, A:R.1207 pi-Cation interactions: A:R.994, A:R.1027

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jouravleva, K. et al., Structural basis of microRNA biogenesis by Dicer-1 and its partner protein Loqs-PB. Mol.Cell (2022)

Release Date

2022-11-16

Peptides

Endoribonuclease Dcr-1: A
Loquacious, isoform B: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
K

Endoribonuclease Dcr-1

Loquacious, isoform B

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