Research workbench
Crystal structure of the active catalytic core of the human dead-box protein DDX3
Analyse Crystal structure of the active catalytic core of the human dead-box protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5E7I
- Type
- protein
- Length
- 1,272 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent RNA helicase DDX3X
- EC
- 3.6.4.13
- UniProt
- O00571
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | ATP-dependent RNA helicase DDX3X (EC 3.6.4.13) | protein | 418 | 40% helix, 16% strand | O00571 |
| A | ATP-dependent RNA helicase DDX3X (EC 3.6.4.13) | protein | 430 | 42% helix, 16% strand | O00571 |
| C | ATP-dependent RNA helicase DDX3X (EC 3.6.4.13) | protein | 424 | 40% helix, 16% strand | O00571 |
Pockets
20 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1093 | 0.82 | 0.84 | 131 | empty |
| 2 | 945 | 0.80 | 0.82 | 96 | empty |
| 3 | 345 | 0.69 | 0.83 | 50 | empty |
| 4 | 238 | 0.68 | 0.85 | 49 | empty |
| 5 | 220 | 0.52 | 0.77 | 28 | empty |
Interfaces
3 interfaces between chains.
- B–C · 738 Ų buried · 2 hydrogen bonds · protein-protein
- B–A · 453 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 322 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5E7I · Crystal structure of the active catalytic core of the human DEAD-box protein DDX3 · the same entry in another collection · chain B against B, TM-score 1.00
- O00571 · AlphaFold monomer V2.0 prediction for ATP-dependent RNA helicase DDX3X (O00571) · a predicted model of the same protein · chain C against A, TM-score 0.78
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 O00571
- Elsewhere: RCSB PDB 5E7I · PDBe 5E7I · UniProt O00571
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