MolNFT v1 · #177531 · protein + RNA

Cryo-EM structure of arabidopsis DCL1 in complex with pri-miRNA 166F

7ELD · Endoribonuclease dicer homolog 1: “Cryo-EM structure of arabidopsis DCL1 in complex with pri-miRNA 166F”. Electron microscopy, 20 pockets (best druggability 0.82). MolNFT v1 #177531 on GenesisL1: 3D structure, binding sites and…

PDB: 7ELD
Type: protein + RNA
Length: 1,246 residues
Chains: 2
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Endoribonuclease dicer homolog 1; Pri-miRNA 166F
EC: 3.1.26.-
UniProt: Q9SP32
Pockets: 20 · best druggability 0.82

Structure

electron microscopy · 2 distinct chains · 50% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Endoribonuclease dicer homolog 1 (EC 3.1.26.-)	protein	1137	50% helix, 8% strand	Q9SP32
B	Pri-miRNA 166F	rna	109	—	—

Pockets

20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	846	0.82	0.84	87	empty
2	616	0.80	0.86	69	empty
3	895	0.80	0.82	81	empty
4	820	0.73	0.79	46	empty
5	558	0.71	0.81	37	empty

Interfaces

1 interface between chains.

A–B · 3388 Å² buried · 82 hydrogen bonds · protein-nucleic

Compared structures

7ELD · Cryo-EM structure of Arabidopsis DCL1 in complex with pri-miRNA 166f · the same entry in another collection · chain A against A, TM-score 1.00
Q9SP32 · AlphaFold monomer V2.0 prediction for endoribonuclease dicer homolog 1 (Q9SP32) · a predicted model of the same protein · chain A against A, TM-score 0.50

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q9SP32
Elsewhere: RCSB PDB 7ELD · PDBe 7ELD · UniProt Q9SP32

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