MolNFT v1 · #50194 · protein
Crystal structure of the helicase domain of human DDX25 RNA helicase
2RB4 · ATP-dependent RNA helicase DDX25: “Crystal structure of the helicase domain of human DDX25 RNA helicase”. X-ray diffraction, 3 ligands (ZN, CL, SO4), 3 pockets (best druggability 0.70). MolNFT v1 #50194 on GenesisL1: 3D structure…
- PDB
- 2RB4
- Type
- protein
- Length
- 327 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent RNA helicase DDX25
- EC
- 3.6.1.-
- UniProt
- Q9UHL0
- Ligands
- ZN, CL, SO4
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent RNA helicase DDX25 (EC 3.6.1.-) | protein | 164 | 35% helix, 23% strand | Q9UHL0 |
| B | ATP-dependent RNA helicase DDX25 (EC 3.6.1.-) | protein | 163 | 36% helix, 24% strand | Q9UHL0 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 539 | 0.70 | 0.79 | 78 | empty |
| 2 | 74 | 0.32 | 0.75 | 17 | CL |
| 3 | 50 | 0.24 | 0.73 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 984 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 2RB4 · Crystal structure of the Helicase domain of human DDX25 RNA helicase · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UHL0 · AlphaFold monomer V2.0 prediction for ATP-dependent RNA helicase DDX25 (Q9UHL0) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 Q9UHL0
- Elsewhere: RCSB PDB 2RB4 · PDBe 2RB4 · UniProt Q9UHL0
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