Research workbench
Crystal structure of DHX8 helicase domain bound to ADP at 2.3 ångström
Analyse Crystal structure of DHX8 helicase domain bound to ADP at 2.3 ångström in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HYT
- Type
- protein
- Length
- 2,528 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent RNA helicase DHX8
- EC
- 3.6.4.13
- UniProt
- Q14562
- Ligands
- ADP, MG, CL
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent RNA helicase DHX8 (EC 3.6.4.13) | protein | 632 | 43% helix, 19% strand | Q14562 |
| B | ATP-dependent RNA helicase DHX8 (EC 3.6.4.13) | protein | 634 | 43% helix, 19% strand | Q14562 |
| C | ATP-dependent RNA helicase DHX8 (EC 3.6.4.13) | protein | 632 | 43% helix, 20% strand | Q14562 |
| D | ATP-dependent RNA helicase DHX8 (EC 3.6.4.13) | protein | 630 | 43% helix, 20% strand | Q14562 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- DMS · Dimethyl sulfoxide · additive · 18 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, D, B, C
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 775 | 0.82 | 0.85 | 90 | empty |
| 2 | 447 | 0.80 | 0.88 | 65 | ADP, MG |
| 3 | 537 | 0.79 | 0.86 | 67 | ADP, MG |
| 4 | 944 | 0.78 | 0.81 | 104 | empty |
| 5 | 497 | 0.77 | 0.84 | 59 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1728 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 1580 Ų buried · 27 hydrogen bonds · protein-protein
- A–D · 687 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 675 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6HYT · Crystal structure of DHX8 helicase domain bound to ADP at 2.3 Angstrom · the same entry in another collection · chain D against D, TM-score 1.00
- Q14562 · AlphaFold monomer V2.0 prediction for ATP-dependent RNA helicase DHX8 (Q14562) · a predicted model of the same protein · chain B against A, TM-score 0.94
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 Q14562
- Elsewhere: RCSB PDB 6HYT · PDBe 6HYT · UniProt Q14562
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