MolNFT v1 · #120299 · protein
Crystal structure of the DDX41 dead domain in an apo open form
5GVS · Probable ATP-dependent RNA helicase DDX41: “Crystal structure of the DDX41 dead domain in an apo open form”. X-ray diffraction, 13 pockets (best druggability 0.75). MolNFT v1 #120299 on GenesisL1: 3D structure, binding sites and…
- 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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