Research workbench
Human dead-box RNA-helicase DDX19 in complex with ADP
Analyse Human dead-box RNA-helicase DDX19 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
- 3EWS
- Type
- protein
- Length
- 821 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent RNA helicase DDX19B
- EC
- 3.6.1.-
- UniProt
- Q9UMR2
- Ligands
- ADP
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent RNA helicase DDX19B (EC 3.6.1.-) | protein | 416 | 38% helix, 17% strand | Q9UMR2 |
| B | ATP-dependent RNA helicase DDX19B (EC 3.6.1.-) | protein | 405 | 39% helix, 16% strand | Q9UMR2 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 911 | 0.77 | 0.80 | 79 | ADP |
| 2 | 733 | 0.77 | 0.81 | 100 | empty |
| 3 | 683 | 0.75 | 0.81 | 65 | ADP |
| 4 | 412 | 0.69 | 0.81 | 43 | empty |
| 5 | 182 | 0.49 | 0.77 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1235 Ų buried · 16 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 Q9UMR2
- Elsewhere: RCSB PDB 3EWS · PDBe 3EWS · UniProt Q9UMR2
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