Research workbench
Cryo-EM structure of human dicer and its complexes with a pre-miRNA substrate
Analyse Cryo-EM structure of human dicer and its complexes with a pre-miRNA substrate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZAK
- Type
- protein
- Length
- 1,389 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endoribonuclease dicer; Risc-loading complex subunit TARBP2
- EC
- 3.1.26.3
- UniProt
- Q9UPY3, Q15633
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 2 distinct chains · 41% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endoribonuclease dicer (EC 3.1.26.3) | protein | 1314 | 41% helix, 8% strand | Q9UPY3 |
| B | Risc-loading complex subunit TARBP2 | protein | 75 | 39% helix, 16% strand | Q15633 |
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 292 | 0.80 | 0.91 | 49 | empty |
| 2 | 272 | 0.80 | 0.91 | 42 | empty |
| 3 | 922 | 0.79 | 0.81 | 100 | empty |
| 4 | 110 | 0.78 | 0.96 | 20 | empty |
| 5 | 1076 | 0.78 | 0.80 | 85 | empty |
Interfaces
1 interface between chains.
- A–B · 1122 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5ZAK · 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 0.86
- Q9UPY3 · AlphaFold monomer V2.0 prediction for endoribonuclease dicer (Q9UPY3) · a predicted model of the same protein · chain A against A, TM-score 0.82
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 5ZAK · PDBe 5ZAK · UniProt Q9UPY3 · UniProt Q15633
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