Research workbench
DDX3X bound to ATP analog and remodeled RNA:DNA hybrid
Analyse DDX3X bound to ATP analog and remodeled RNA:DNA hybrid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LIU
- Type
- protein + RNA
- Length
- 912 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent RNA helicase DDX3X; 5'-R(*GP*GP*GP*CP*GP*GP*G)-D(P*CP*CP*CP*GP*CP*CP*C)-3'
- EC
- 3.6.4.13
- UniProt
- O00571
- Ligands
- 08T, MG
- Pockets
- 15 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ATP-dependent RNA helicase DDX3X (EC 3.6.4.13) | protein | 442 | 41% helix, 16% strand | O00571 |
| X, Y | 5'-R(*GP*GP*GP*CP*GP*GP*G)-D(P*CP*CP*CP*GP*CP*CP*C)-3' | rna | 14 | — | — |
Ligands and binding sites
- 08T · [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 739 | 0.75 | 0.80 | 73 | MG, 08T |
| 2 | 577 | 0.75 | 0.82 | 64 | MG, 08T |
| 3 | 393 | 0.62 | 0.77 | 47 | empty |
| 4 | 427 | 0.55 | 0.73 | 44 | empty |
| 5 | 125 | 0.47 | 0.78 | 19 | empty |
Interfaces
6 interfaces between chains.
- B–Y · 727 Ų buried · 28 hydrogen bonds · protein-nucleic
- A–X · 709 Ų buried · 28 hydrogen bonds · protein-nucleic
- A–B · 707 Ų buried · 16 hydrogen bonds · protein-protein
- X–Y · 427 Ų buried · 53 hydrogen bonds · nucleic-nucleic
- A–Y · 58 Ų buried · 1 hydrogen bond · protein-nucleic
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 O00571
- Elsewhere: RCSB PDB 7LIU · PDBe 7LIU · UniProt O00571
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