MolNFT v1 · #141534 · protein + RNA

Cryo-EM structure of human dicer and its complexes with a pre-miRNA substrate

5ZAM · Endoribonuclease dicer: “Cryo-EM structure of human dicer and its complexes with a pre-miRNA substrate”. Electron microscopy, 20 pockets (best druggability 0.85). MolNFT v1 #141534 on GenesisL1: 3D structure, binding sites and…

PDB: 5ZAM
Type: protein + RNA
Length: 1,433 residues
Chains: 3
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Endoribonuclease dicer; Risc-loading complex subunit TARBP2; RNA (73-mer)
EC: 3.1.26.3
UniProt: Q9UPY3, Q15633
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 3 distinct chains · 42% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Endoribonuclease dicer (EC 3.1.26.3)	protein	1314	42% helix, 7% strand	Q9UPY3
B	Risc-loading complex subunit TARBP2	protein	75	41% helix, 19% strand	Q15633
C	RNA (73-mer)	rna	44	—	—

Pockets

20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	353	0.85	0.94	48	empty
2	1116	0.83	0.83	134	empty
3	1035	0.83	0.83	111	empty
4	98	0.77	0.96	21	empty
5	201	0.75	0.90	37	empty

Interfaces

2 interfaces between chains.

A–C · 1303 Å² buried · 36 hydrogen bonds · protein-nucleic
A–B · 1135 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

5ZAM · Cryo-EM structure of human Dicer and its complexes with a pre-miRNA substrate · the same entry in another collection · chain A against A, TM-score 1.00
Q15633 · AlphaFold monomer V2.0 prediction for risc-loading complex subunit TARBP2 (Q15633) · a predicted model of the same protein · chain B against A, TM-score 0.84
Q9UPY3 · AlphaFold monomer V2.0 prediction for endoribonuclease dicer (Q9UPY3) · a predicted model of the same protein · chain A against A, TM-score 0.81

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 Q9UPY3
Every structure of UniProt Q15633
Elsewhere: RCSB PDB 5ZAM · PDBe 5ZAM · UniProt Q9UPY3 · UniProt Q15633

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