MolNFT v1 · #145816 · protein
Crystal structure of small molecule AMP-acrylamide covalently bound to DDX3 S228C
6CZ5 · ATP-dependent RNA helicase DDX3X: “Crystal structure of small molecule AMP-acrylamide covalently bound to DDX3 S228C”. X-ray diffraction, 1 ligand (FPJ), 5 pockets (best druggability 0.64). MolNFT v1 #145816 on GenesisL1: 3D…
- PDB
- 6CZ5
- Type
- protein
- Length
- 427 residues
- Chains
- 1
- 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
- FPJ
- Pockets
- 5 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent RNA helicase DDX3X (EC 3.6.4.13) | protein | 427 | 39% helix, 17% strand | O00571 |
Ligands and binding sites
- FPJ · 5'-O-[(R)-hydroxy(propanoylamino)phosphoryl]adenosine · 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 | 369 | 0.64 | 0.79 | 48 | FPJ |
| 2 | 266 | 0.53 | 0.76 | 32 | empty |
| 3 | 84 | 0.50 | 0.83 | 24 | empty |
| 4 | 93 | 0.37 | 0.76 | 17 | empty |
| 5 | 82 | 0.32 | 0.74 | 15 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6CZ5 · Crystal structure of small molecule AMP-acrylamide covalently bound to DDX3 S228C · 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 0.77
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 6CZ5 · PDBe 6CZ5 · UniProt O00571
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