Research workbench
Crystal structure of RNA helicase DDX17 in complex of RU10 RNA
Analyse Crystal structure of RNA helicase DDX17 in complex of RU10 RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UV1
- Type
- protein + RNA
- Length
- 886 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable ATP-dependent RNA helicase DDX17; RNA RU10
- EC
- 3.6.4.13
- UniProt
- Q92841
- Ligands
- ADP, BEF, MG
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable ATP-dependent RNA helicase DDX17 (EC 3.6.4.13) | protein | 438 | 42% helix, 15% strand | Q92841 |
| B | Probable ATP-dependent RNA helicase DDX17 (EC 3.6.4.13) | protein | 434 | 41% helix, 15% strand | Q92841 |
| C, D | RNA RU10 | rna | 7 | — | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- BEF · Beryllium trifluoride ion · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 10 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 569 | 0.71 | 0.80 | 85 | MG |
| 2 | 527 | 0.69 | 0.79 | 76 | ADP, BEF, MG |
| 3 | 535 | 0.68 | 0.78 | 85 | ADP, BEF, MG |
| 4 | 126 | 0.55 | 0.83 | 22 | empty |
| 5 | 75 | 0.34 | 0.76 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 839 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 657 Ų buried · 29 hydrogen bonds · protein-nucleic
- B–D · 639 Ų buried · 25 hydrogen bonds · protein-nucleic
Compared structures
- 6UV1 · Crystal structure of RNA helicase DDX17 in complex of rU10 RNA · the same entry in another collection · chain A against A, TM-score 1.00
- Q92841 · AlphaFold monomer V2.0 prediction for probable ATP-dependent RNA helicase DDX17 (Q92841) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q92841
- Elsewhere: RCSB PDB 6UV1 · PDBe 6UV1 · UniProt Q92841
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