Research workbench
Human dead-box RNA helicase DDX5 (P68), conserved domain I in complex with ADP
Analyse Human dead-box RNA helicase DDX5 (P68), conserved domain I in complex with ADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FE2
- Type
- protein
- Length
- 468 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable ATP-dependent RNA helicase DDX5
- EC
- 3.6.1.-
- UniProt
- P17844
- Ligands
- ADP, SO4, CL
- Pockets
- 4 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Probable ATP-dependent RNA helicase DDX5 (EC 3.6.1.-) | protein | 234 | 44% helix, 15% strand | P17844 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- CL · Chloride ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 472 | 0.61 | 0.75 | 54 | empty |
| 2 | 59 | 0.41 | 0.81 | 18 | empty |
| 3 | 117 | 0.41 | 0.75 | 20 | ADP |
| 4 | 76 | 0.36 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 693 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 3FE2 · Human DEAD-BOX RNA helicase DDX5 (P68), conserved domain I in complex with ADP · the same entry in another collection · chain A against A, TM-score 1.00
- P17844 · AlphaFold monomer V2.0 prediction for probable ATP-dependent RNA helicase DDX5 (P17844) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P17844
- Elsewhere: RCSB PDB 3FE2 · PDBe 3FE2 · UniProt P17844
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.