Research workbench
Crystal structure of the core domain of RNA helicase DDX17 with RNA pri-125A-OLIGO2
Analyse Crystal structure of the core domain of RNA helicase DDX17 with RNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UV3
- Type
- protein + RNA
- Length
- 432 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable ATP-dependent RNA helicase DDX17; 125A-OLIGO2
- EC
- 3.6.4.13
- UniProt
- Q92841
- Ligands
- ADP, BEF, MG
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable ATP-dependent RNA helicase DDX17 (EC 3.6.4.13) | protein | 426 | 44% helix, 15% strand | Q92841 |
| B | 125A-OLIGO2 | rna | 6 | — | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- BEF · Beryllium trifluoride ion · ligand · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 450 | 0.65 | 0.78 | 54 | ADP, BEF, MG |
| 2 | 81 | 0.46 | 0.82 | 23 | empty |
| 3 | 125 | 0.45 | 0.78 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 714 Ų buried · 34 hydrogen bonds · protein-nucleic
Compared structures
- 6UV3 · Crystal structure of the core domain of RNA helicase DDX17 with RNA pri-125a-oligo2 · 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 6UV3 · PDBe 6UV3 · UniProt Q92841
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