MolNFT v1 · #189849 · protein + RNA
DICER2-loqspd-dsrna complex at mid-translocation state
7W0D · Loquacious, isoform D: “DICER2-loqspd-dsrna complex at mid-translocation state”. Electron microscopy, 2 ligands (ADP, MG), 20 pockets (best druggability 0.88). MolNFT v1 #189849 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 7W0D
- Type
- protein + RNA
- Length
- 2,337 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Loquacious, isoform D; Dsrna; Dicer-2, isoform a
- EC
- 3.1.21.1, 3.1.26.-, 3.1.26.3, 3.6.1.3
- UniProt
- M9MRT5, A1ZAW0
- Ligands
- ADP, MG
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 5 distinct chains · 47% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Loquacious, isoform D | protein | 16 | 0% helix, 13% strand | M9MRT5 |
| D, C | Dsrna | rna | 52 | — | — |
| G | Loquacious, isoform D | protein | 13 | 0% helix, 15% strand | M9MRT5 |
| A | Dicer-2, isoform a (EC 3.1.21.1, 3.1.26.-, 3.1.26.3, 3.6.1.3) | protein | 1544 | 46% helix, 12% strand | A1ZAW0 |
| F | Dicer-2, isoform a (EC 3.1.21.1, 3.1.26.-, 3.1.26.3, 3.6.1.3) | protein | 660 | 50% helix, 12% strand | A1ZAW0 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, F
- MG · Magnesium ion · metal · 2 copies · chains A, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 704 | 0.88 | 0.92 | 112 | MG |
| 2 | 589 | 0.80 | 0.86 | 65 | empty |
| 3 | 445 | 0.78 | 0.87 | 56 | empty |
| 4 | 349 | 0.78 | 0.88 | 45 | empty |
| 5 | 504 | 0.77 | 0.85 | 62 | empty |
Interfaces
8 interfaces between chains.
- D–C · 2563 Ų buried · 326 hydrogen bonds · nucleic-nucleic
- D–A · 1607 Ų buried · 42 hydrogen bonds · protein-nucleic
- F–C · 1251 Ų buried · 56 hydrogen bonds · protein-nucleic
- B–A · 1121 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 1076 Ų buried · 19 hydrogen bonds · protein-nucleic
Compared structures
- 7W0D · Dicer2-LoqsPD-dsRNA complex at mid-translocation state · the same entry in another collection · chain B against B, 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 M9MRT5
- Every structure of UniProt A1ZAW0
- Elsewhere: RCSB PDB 7W0D · PDBe 7W0D · UniProt M9MRT5 · UniProt A1ZAW0
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