MolNFT v1 · #82825 · protein + RNA
Structural insights into risc assembly facilitated by dsrna binding domains of human RNA helicase a (DHX9)
3VYY · ATP-dependent RNA helicase a: “Structural insights into risc assembly facilitated by dsrna binding domains of human RNA helicase a (DHX9)”. X-ray diffraction, 1 pocket (best druggability 0.74). MolNFT v1 #82825 on GenesisL1: 3D…
- PDB
- 3VYY
- Type
- protein + RNA
- Length
- 220 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent RNA helicase a; RNA (5'-R(*GP*CP*GP*CP*GP*CP*GP*CP*GP*C)-3')
- EC
- 3.6.4.13
- UniProt
- Q08211
- Pockets
- 1 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent RNA helicase a (EC 3.6.4.13) | protein | 86 | 37% helix, 27% strand | Q08211 |
| B | ATP-dependent RNA helicase a (EC 3.6.4.13) | protein | 84 | 40% helix, 23% strand | Q08211 |
| C, D, E, F, G | RNA (5'-R(*GP*CP*GP*CP*GP*CP*GP*CP*GP*C)-3') | rna | 10 | — | — |
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1129 | 0.74 | 0.78 | 72 | empty |
Interfaces
16 interfaces between chains.
- C–D · 494 Ų buried · 53 hydrogen bonds · nucleic-nucleic
- E–F · 492 Ų buried · 50 hydrogen bonds · nucleic-nucleic
- B–D · 290 Ų buried · 6 hydrogen bonds · protein-nucleic
- A–F · 283 Ų buried · 3 hydrogen bonds · protein-nucleic
- A–D · 270 Ų buried · 4 hydrogen bonds · protein-nucleic
Compared structures
- 3VYY · Structural insights into RISC assembly facilitated by dsRNA binding domains of human RNA… · the same entry in another collection · chain G against G, TM-score 1.00
- Q08211 · AlphaFold monomer V2.0 prediction for ATP-dependent RNA helicase a (Q08211) · a predicted model of the same protein · chain B against A, TM-score 0.94
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 Q08211
- Elsewhere: RCSB PDB 3VYY · PDBe 3VYY · UniProt Q08211
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