Research workbench
Structure of the dicer-2-R2D2 heterodimer bound to small RNA duplex
Analyse Structure of the dicer-2-R2D2 heterodimer bound to small RNA duplex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7V6C
- Type
- protein + RNA
- Length
- 1,852 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dicer-2, isoform a; R2D2; RNA (5'-R(P*UP*GP*AP*GP*G)-3'); RNA…
- EC
- 3.1.21.1, 3.1.26.-, 3.1.26.3, 3.6.1.3
- UniProt
- A1ZAW0, Q9VLW8
- Pockets
- 20 · best druggability 0.76
Structure
electron microscopy · 6 distinct chains · 45% helix, 13% 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 | 1540 | 45% helix, 12% strand | A1ZAW0 |
| B | R2D2 | protein | 260 | 45% helix, 22% strand | Q9VLW8 |
| E | RNA (5'-R(P*UP*GP*AP*GP*G)-3') | rna | 5 | — | — |
| F | RNA (5'-R(P*CP*CP*UP*CP*UP*CP*U)-3') | rna | 7 | — | — |
| C | RNA (5'- R(*AP*UP*GP*AP*GP*GP*UP*AP*GP*UP*AP*GP*GP*UP*UP*GP*UP*AP*UP*AP*G)- 3') | rna | 20 | — | — |
| D | RNA (5'- R(*CP*UP*AP*UP*AP*CP*AP*AP*CP*CP*UP*AP*CP*UP*AP*CP*CP*UP*CP*UP*C)- 3') | rna | 20 | — | — |
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 | 273 | 0.76 | 0.89 | 48 | empty |
| 2 | 755 | 0.70 | 0.77 | 71 | empty |
| 3 | 763 | 0.68 | 0.76 | 33 | empty |
| 4 | 433 | 0.66 | 0.79 | 32 | empty |
| 5 | 325 | 0.65 | 0.81 | 38 | empty |
Interfaces
9 interfaces between chains.
- A–B · 2518 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 941 Ų buried · 88 hydrogen bonds · nucleic-nucleic
- B–D · 677 Ų buried · 14 hydrogen bonds · protein-nucleic
- B–C · 596 Ų buried · 9 hydrogen bonds · protein-nucleic
- E–F · 271 Ų buried · 26 hydrogen bonds · nucleic-nucleic
Compared structures
- 7V6C · Structure of the Dicer-2-R2D2 heterodimer bound to small RNA duplex · 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 Q9VLW8
- Elsewhere: RCSB PDB 7V6C · PDBe 7V6C · UniProt A1ZAW0 · UniProt Q9VLW8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.