MolNFT v1 · #189851 · protein + RNA
DMDICER2-loqspd-dsrna post-dicing status
7W0F · Dicer-2, isoform a: “DMDICER2-loqspd-dsrna post-dicing status”. Electron microscopy, 20 pockets (best druggability 0.81). MolNFT v1 #189851 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7W0F
- Type
- protein + RNA
- Length
- 1,586 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dicer-2, isoform a; Loquacious, isoform D; SiRNA
- EC
- 3.1.21.1, 3.1.26.-, 3.1.26.3, 3.6.1.3
- UniProt
- A1ZAW0, M9MRT5
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 6 distinct chains · 47% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dicer-2, isoform a (EC 3.1.21.1, 3.1.26.-, 3.1.26.3, 3.6.1.3) | protein | 1476 | 47% helix, 12% strand | A1ZAW0 |
| B | Loquacious, isoform D | protein | 16 | 0% helix, 13% strand | M9MRT5 |
| C | SiRNA | rna | 21 | — | — |
| D | SiRNA | rna | 21 | — | — |
| E | SiRNA | rna | 26 | — | — |
| F | SiRNA | rna | 26 | — | — |
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 392 | 0.81 | 0.90 | 58 | empty |
| 2 | 590 | 0.81 | 0.87 | 66 | empty |
| 3 | 1071 | 0.81 | 0.82 | 82 | empty |
| 4 | 1195 | 0.80 | 0.82 | 91 | empty |
| 5 | 703 | 0.78 | 0.83 | 64 | empty |
Interfaces
7 interfaces between chains.
- A–F · 1406 Ų buried · 38 hydrogen bonds · protein-nucleic
- E–F · 1156 Ų buried · 118 hydrogen bonds · nucleic-nucleic
- A–B · 1100 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 1040 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–D · 1002 Ų buried · 31 hydrogen bonds · protein-nucleic
Compared structures
- 7W0F · dmDicer2-LoqsPD-dsRNA Post-dicing status · the same entry in another collection · chain A against A, TM-score 1.00
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 A1ZAW0
- Every structure of UniProt M9MRT5
- Elsewhere: RCSB PDB 7W0F · PDBe 7W0F · UniProt A1ZAW0 · UniProt M9MRT5
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