Research workbench
Crystal structure of the DDX41 dead domain in complex with SO42- and MG2+
Analyse Crystal structure of the DDX41 dead domain in complex with SO42- and MG2+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5H1Y
- Type
- protein
- Length
- 487 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable ATP-dependent RNA helicase DDX41
- EC
- 3.6.4.13
- UniProt
- Q9UJV9
- Ligands
- MG, SO4
- Pockets
- 2 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable ATP-dependent RNA helicase DDX41 (EC 3.6.4.13) | protein | 242 | 44% helix, 14% strand | Q9UJV9 |
| B | Probable ATP-dependent RNA helicase DDX41 (EC 3.6.4.13) | protein | 245 | 45% helix, 13% strand | Q9UJV9 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 335 | 0.63 | 0.79 | 52 | empty |
| 2 | 66 | 0.30 | 0.74 | 18 | SO4, MG |
Interfaces
1 interface between chains.
- A–B · 229 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5H1Y · Crystal structure of the DDX41 DEAD domain in complex with SO42- and Mg2+ · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UJV9 · AlphaFold monomer V2.0 prediction for probable ATP-dependent RNA helicase DDX41 (Q9UJV9) · 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 Q9UJV9
- Elsewhere: RCSB PDB 5H1Y · PDBe 5H1Y · UniProt Q9UJV9
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