MolNFT v1 · #189850 · protein + RNA
DMDICER2-loqspd-dsrna active-dicing status
7W0E: “DMDICER2-loqspd-dsrna active-dicing status”. Electron microscopy, 2 ligands (ADP, MG), 20 pockets (best druggability 0.81). MolNFT v1 #189850 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7W0E
- Type
- protein + RNA
- Length
- 1,661 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dsrna; Dicer-2, isoform a; Loquacious, isoform D
- 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 0.81
Structure
electron microscopy · 3 distinct chains · 44% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | Dsrna | rna | 52 | — | — |
| A | Dicer-2, isoform a (EC 3.1.21.1, 3.1.26.-, 3.1.26.3, 3.6.1.3) | protein | 1541 | 45% helix, 12% strand | A1ZAW0 |
| B | Loquacious, isoform D | protein | 16 | 0% helix, 13% strand | M9MRT5 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- MG · Magnesium ion · metal · 3 copies · chains D, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 437 | 0.81 | 0.90 | 64 | empty |
| 2 | 376 | 0.80 | 0.89 | 44 | empty |
| 3 | 517 | 0.79 | 0.86 | 56 | empty |
| 4 | 764 | 0.79 | 0.82 | 69 | MG, ADP |
| 5 | 175 | 0.77 | 0.94 | 28 | empty |
Interfaces
4 interfaces between chains.
- D–A · 2810 Ų buried · 58 hydrogen bonds · protein-nucleic
- C–D · 2365 Ų buried · 201 hydrogen bonds · nucleic-nucleic
- C–A · 2056 Ų buried · 27 hydrogen bonds · protein-nucleic
- A–B · 1094 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7W0E · dmDicer2-LoqsPD-dsRNA Active-dicing status · the same entry in another collection · chain C against C, 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 7W0E · PDBe 7W0E · UniProt A1ZAW0 · UniProt M9MRT5
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