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
- 5ZAL
- Type
- protein + RNA
- Length
- 1,447 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 0.82
Structure
electron microscopy · 3 distinct chains · 39% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endoribonuclease dicer (EC 3.1.26.3) | protein | 1314 | 39% helix, 8% strand | Q9UPY3 |
| B | Risc-loading complex subunit TARBP2 | protein | 75 | 27% helix, 17% strand | Q15633 |
| C | RNA (73-mer) | rna | 58 | — | — |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 295 | 0.82 | 0.93 | 43 | empty |
| 2 | 196 | 0.80 | 0.94 | 33 | empty |
| 3 | 584 | 0.78 | 0.84 | 61 | empty |
| 4 | 99 | 0.77 | 0.97 | 26 | empty |
| 5 | 362 | 0.77 | 0.87 | 41 | empty |
Interfaces
2 interfaces between chains.
- A–C · 1472 Ų buried · 38 hydrogen bonds · protein-nucleic
- A–B · 1105 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5ZAL · 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
- 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
- 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 0.79
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 5ZAL · PDBe 5ZAL · UniProt Q9UPY3 · UniProt Q15633
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