MolNFT v1 · #148545 · protein
Crystal structure of the C-terminal reca domain of DDX6 in complex with a conserved peptide from LSM14
6F9S · Probable ATP-dependent RNA helicase DDX6: “Crystal structure of the C-terminal reca domain of DDX6 in complex with a conserved peptide from LSM14”. X-ray diffraction, 1 ligand (SO4), 3 pockets (best druggability 0.41). MolNFT v1…
- PDB
- 6F9S
- Type
- protein
- Length
- 210 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable ATP-dependent RNA helicase DDX6; Cytokinesis, apoptosis, RNA-associated
- EC
- 3.6.4.13
- UniProt
- P26196, Q9XW17
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.41
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable ATP-dependent RNA helicase DDX6 (EC 3.6.4.13) | protein | 167 | 38% helix, 23% strand | P26196 |
| B | Cytokinesis, apoptosis, RNA-associated | protein | 43 | 65% helix, 0% strand | Q9XW17 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 158 | 0.41 | 0.74 | 22 | empty |
| 2 | 57 | 0.37 | 0.79 | 16 | empty |
| 3 | 51 | 0.28 | 0.74 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1386 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6F9S · Crystal structure of the C-terminal RecA domain of DDX6 in complex with a conserved… · the same entry in another collection · chain A against A, TM-score 1.00
- P26196 · AlphaFold monomer V2.0 prediction for probable ATP-dependent RNA helicase DDX6 (P26196) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 P26196
- Every structure of UniProt Q9XW17
- Elsewhere: RCSB PDB 6F9S · PDBe 6F9S · UniProt P26196 · UniProt Q9XW17
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