Research workbench
DICER2-loqs-pd-dsrna complex at early-translocation state
Analyse DICER2-loqs-pd-dsrna complex at early-translocation state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7W0C
- Type
- protein + RNA
- Length
- 1,564 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dicer-2, isoform a; Loquacious, isoform D; RNA (35-mer)
- EC
- 3.1.21.1, 3.1.26.-, 3.1.26.3, 3.6.1.3
- UniProt
- A1ZAW0, M9MRT5
- Ligands
- ADP, MG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 4 distinct chains · 47% helix, 11% 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 | 48% helix, 11% strand | A1ZAW0 |
| B | Loquacious, isoform D | protein | 16 | 0% helix, 6% strand | M9MRT5 |
| C | RNA (35-mer) | rna | 35 | — | — |
| D | RNA (35-mer) | rna | 37 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 741 | 0.83 | 0.86 | 69 | empty |
| 2 | 147 | 0.77 | 0.95 | 33 | empty |
| 3 | 381 | 0.77 | 0.87 | 67 | empty |
| 4 | 512 | 0.74 | 0.83 | 63 | empty |
| 5 | 308 | 0.74 | 0.86 | 47 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1692 Ų buried · 192 hydrogen bonds · nucleic-nucleic
- A–D · 1152 Ų buried · 27 hydrogen bonds · protein-nucleic
- A–B · 1106 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 948 Ų buried · 18 hydrogen bonds · protein-nucleic
Compared structures
- 7W0C · Dicer2-Loqs-PD-dsRNA complex at early-translocation state · 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 7W0C · PDBe 7W0C · UniProt A1ZAW0 · UniProt M9MRT5
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