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Crystal structure of DDX53 dead-box domain
Analyse Crystal structure of DDX53 dead-box domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IUY
- Type
- protein
- Length
- 419 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable ATP-dependent RNA helicase DDX53
- EC
- 3.6.1.-
- UniProt
- Q86TM3
- Ligands
- AMP, CL
- Pockets
- 3 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable ATP-dependent RNA helicase DDX53 (EC 3.6.1.-) | protein | 213 | 43% helix, 16% strand | Q86TM3 |
| B | Probable ATP-dependent RNA helicase DDX53 (EC 3.6.1.-) | protein | 206 | 43% helix, 17% strand | Q86TM3 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- CL · Chloride 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 197 | 0.66 | 0.85 | 35 | empty |
| 2 | 183 | 0.53 | 0.78 | 22 | empty |
| 3 | 177 | 0.46 | 0.75 | 26 | CL |
Interfaces
1 interface between chains.
- A–B · 746 Ų buried · 11 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 Q86TM3
- Elsewhere: RCSB PDB 3IUY · PDBe 3IUY · UniProt Q86TM3
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