MolNFT v1 · #103989 · protein
Dead-box RNA helicase DDX3X domain 1 with N-terminal ATP-binding loop
4PX9 · ATP-dependent RNA helicase DDX3X: “Dead-box RNA helicase DDX3X domain 1 with N-terminal ATP-binding loop”. X-ray diffraction, 1 ligand (ADP), 9 pockets (best druggability 0.81). MolNFT v1 #103989 on GenesisL1: 3D structure, binding…
- PDB
- 4PX9
- Type
- protein
- Length
- 797 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
- Ligands
- ADP
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ATP-dependent RNA helicase DDX3X (EC 3.6.4.13) | protein | 262 | 42% helix, 16% strand | O00571 |
| C | ATP-dependent RNA helicase DDX3X (EC 3.6.4.13) | protein | 273 | 40% helix, 15% strand | O00571 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 837 | 0.81 | 0.84 | 108 | ADP |
| 2 | 134 | 0.61 | 0.86 | 32 | empty |
| 3 | 174 | 0.51 | 0.78 | 28 | empty |
| 4 | 157 | 0.49 | 0.78 | 26 | empty |
| 5 | 94 | 0.49 | 0.82 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 836 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 350 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 222 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4PX9 · DEAD-box RNA helicase DDX3X Domain 1 with N-terminal ATP-binding Loop · the same entry in another collection · chain A against A, 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 B against A, TM-score 0.98
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 4PX9 · PDBe 4PX9 · UniProt O00571
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