Research workbench
DDX18 dead-domain
Analyse DDX18 dead-domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LY5
- Type
- protein
- Length
- 424 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent RNA helicase DDX18
- EC
- 3.6.1.-
- UniProt
- Q9NVP1
- Ligands
- MG, SCN, PO4
- Pockets
- 2 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent RNA helicase DDX18 (EC 3.6.1.-) | protein | 211 | 48% helix, 13% strand | Q9NVP1 |
| B | ATP-dependent RNA helicase DDX18 (EC 3.6.1.-) | protein | 213 | 46% helix, 13% strand | Q9NVP1 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
- SCN · Thiocyanate ion · ion · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 90 | 0.76 | 0.97 | 25 | SCN |
| 2 | 86 | 0.35 | 0.75 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 508 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
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 Q9NVP1
- Elsewhere: RCSB PDB 3LY5 · PDBe 3LY5 · UniProt Q9NVP1
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