Research workbench
Crystal structure of the active catalytic core of the human DEAD-box protein DDX3 bound to AMPPNP
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
- 5E7M
- Type
- protein
- Length
- 424 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.304
- Source
- Homo sapiens
- Molecule
- ATP-dependent RNA helicase DDX3X
- EC
- 3.6.4.13
- UniProt
- O00571
- Ligands
- ANP
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · resolution 2.304 · 1 distinct chain · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent RNA helicase DDX3X (EC 3.6.4.13) | protein | 424 | 41% helix, 16% strand | O00571 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 320 | 0.70 | 0.84 | 42 | ANP |
| 2 | 227 | 0.53 | 0.77 | 34 | empty |
| 3 | 162 | 0.46 | 0.76 | 17 | empty |
| 4 | 95 | 0.38 | 0.76 | 17 | empty |
| 5 | 99 | 0.34 | 0.73 | 20 | empty |
Compared structures
- 5E7M · Crystal structure of the active catalytic core of the human dead-box protein DDX3 bound… · 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 A 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 5E7M · PDBe 5E7M · UniProt O00571
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