Research workbench
Crystal structure of the DDX41 dead domain in an apo open form
Analyse Crystal structure of the DDX41 dead domain in an apo open form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GVS
- Type
- protein
- Length
- 826 residues
- Chains
- 4
- 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
- Pockets
- 13 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable ATP-dependent RNA helicase DDX41 (EC 3.6.4.13) | protein | 216 | 43% helix, 16% strand | Q9UJV9 |
| B | Probable ATP-dependent RNA helicase DDX41 (EC 3.6.4.13) | protein | 215 | 41% helix, 16% strand | Q9UJV9 |
| C | Probable ATP-dependent RNA helicase DDX41 (EC 3.6.4.13) | protein | 198 | 41% helix, 15% strand | Q9UJV9 |
| D | Probable ATP-dependent RNA helicase DDX41 (EC 3.6.4.13) | protein | 197 | 42% helix, 15% strand | Q9UJV9 |
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 402 | 0.75 | 0.85 | 42 | empty |
| 2 | 510 | 0.65 | 0.77 | 53 | empty |
| 3 | 211 | 0.62 | 0.82 | 28 | empty |
| 4 | 60 | 0.53 | 0.87 | 15 | empty |
| 5 | 57 | 0.53 | 0.88 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–C · 925 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 423 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5GVS · Crystal structure of the DDX41 DEAD domain in an apo open form · the same entry in another collection · chain D against D, 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 D against A, TM-score 0.92
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 5GVS · PDBe 5GVS · UniProt Q9UJV9
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