Research workbench
Crystal structure of DEAD-box RNA helicase DDX3X at pre-unwound state
Analyse Crystal structure of DEAD-box RNA helicase DDX3X at pre-unwound state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6O5F
- Type
- protein + RNA
- Length
- 881 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.504
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- ATP-dependent RNA helicase DDX3X; RNA (5'-R(P*CP*AP*AP*GP*GP*UP*CP*AP*UP*UP*CP*GP*CP*AP*AP…
- EC
- 3.6.4.13
- UniProt
- O00571
- Ligands
- CL
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · resolution 2.504 · 3 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ATP-dependent RNA helicase DDX3X (EC 3.6.4.13) | protein | 417 | 44% helix, 17% strand | O00571 |
| C | RNA (5'-R(P*CP*AP*AP*GP*GP*UP*CP*AP*UP*UP*CP*GP*CP*AP*AP*GP*AP*GP*UP*GP*GP*CP*C)-3') | rna | 23 | — | — |
| D | RNA (5'-R(P*CP*AP*AP*GP*GP*UP*CP*AP*UP*UP*CP*GP*CP*AP*AP*GP*AP*GP*UP*GP*GP*CP*C)-3') | rna | 24 | — | — |
Ligands and binding sites
- CL · Chloride ion · ion · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 684 | 0.81 | 0.86 | 75 | empty |
| 2 | 877 | 0.81 | 0.84 | 58 | empty |
| 3 | 291 | 0.73 | 0.87 | 41 | empty |
| 4 | 215 | 0.60 | 0.81 | 34 | empty |
| 5 | 111 | 0.46 | 0.79 | 16 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1072 Ų buried · 111 hydrogen bonds · nucleic-nucleic
- B–D · 673 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–C · 632 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–B · 421 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 345 Ų buried · 5 hydrogen bonds · protein-nucleic
Compared structures
- 6O5F · Crystal structure of dead-box RNA helicase DDX3X at pre-unwound state · the same entry in another collection · chain A against A, TM-score 1.00
- O00571 · AlphaFold monomer V2.0 prediction for ATP-dependent RNA helicase DDX3X (O00571) · a predicted model of the same protein · chain A against A, TM-score 0.61
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 6O5F · PDBe 6O5F · UniProt O00571
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