Research workbench
Crystal structure of DHX8 helicase bound to single stranded poly-adenine RNA
Analyse Crystal structure of DHX8 helicase bound to single stranded poly-adenine RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HYU
- Type
- protein + RNA
- Length
- 1,207 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.22
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- ATP-dependent RNA helicase DHX8; RNA (5'-R(*AP*AP*AP*AP*AP*A)-3'); RNA (5'-R(*A*AP*A)-3')
- EC
- 3.6.4.13
- UniProt
- Q14562
- Pockets
- 17 · best druggability 0.85
Structure
x-ray diffraction · resolution 3.22 · 4 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent RNA helicase DHX8 (EC 3.6.4.13) | protein | 613 | 40% helix, 18% strand | Q14562 |
| B | RNA (5'-R(*AP*AP*AP*AP*AP*A)-3') | rna | 6 | — | — |
| C | ATP-dependent RNA helicase DHX8 (EC 3.6.4.13) | protein | 585 | 42% helix, 17% strand | Q14562 |
| D | RNA (5'-R(*A*AP*A)-3') | rna | 3 | — | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1071 | 0.85 | 0.86 | 92 | empty |
| 2 | 545 | 0.84 | 0.90 | 98 | empty |
| 3 | 650 | 0.78 | 0.83 | 80 | empty |
| 4 | 268 | 0.71 | 0.86 | 33 | empty |
| 5 | 125 | 0.62 | 0.86 | 26 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1132 Ų buried · 28 hydrogen bonds · protein-nucleic
- A–C · 617 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 300 Ų buried · 2 hydrogen bonds · protein-nucleic
Compared structures
- 6HYU · Crystal structure of DHX8 helicase bound to single stranded poly- adenine RNA · the same entry in another collection · chain A against A, TM-score 1.00
- Q14562 · AlphaFold monomer V2.0 prediction for ATP-dependent RNA helicase DHX8 (Q14562) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q14562
- Elsewhere: RCSB PDB 6HYU · PDBe 6HYU · UniProt Q14562
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