MolNFT v1 · #151812 · protein
Crystal structure of DHX8 helicase domain bound to ADP at 2.3 ångström
6HYT · ATP-dependent RNA helicase DHX8: “Crystal structure of DHX8 helicase domain bound to ADP at 2.3 ångström”. X-ray diffraction, 3 ligands (ADP, MG, CL), 20 pockets (best druggability 0.82). MolNFT v1 #151812 on GenesisL1: 3D…
- 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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