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Crystal structure of human DDX19B(AMPPNP)
Analyse Crystal structure of human DDX19B(AMPPNP) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6B4K
- Type
- protein
- Length
- 839 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent RNA helicase DDX19B
- EC
- 3.6.4.13
- UniProt
- Q9UMR2
- Ligands
- ANP, MG
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent RNA helicase DDX19B (EC 3.6.4.13) | protein | 419 | 40% helix, 17% strand | Q9UMR2 |
| B | ATP-dependent RNA helicase DDX19B (EC 3.6.4.13) | protein | 420 | 40% helix, 17% strand | Q9UMR2 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- MLI · Malonate ion · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1072 | 0.78 | 0.80 | 80 | MG, ANP |
| 2 | 795 | 0.77 | 0.81 | 93 | empty |
| 3 | 762 | 0.74 | 0.80 | 66 | MG, ANP |
| 4 | 376 | 0.71 | 0.83 | 34 | empty |
| 5 | 159 | 0.66 | 0.86 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 1317 Ų buried · 19 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 6B4K · PDBe 6B4K · UniProt Q9UMR2
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