Research workbench
DHX36 with an N-terminal truncation bound to ADP-BEF3
Analyse DHX36 with an N-terminal truncation bound to ADP-BEF3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VHC
- Type
- protein
- Length
- 799 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deah (asp-glu-ala-his) box polypeptide 36
- UniProt
- Q05B79
- Ligands
- BEF, ADP, MG
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Deah (asp-glu-ala-his) box polypeptide 36 | protein | 799 | 46% helix, 17% strand | Q05B79 |
Ligands and binding sites
- BEF · Beryllium trifluoride ion · ligand · chains D
- ADP · Adenosine-5'-diphosphate · ligand · chains D
- MG · Magnesium ion · metal · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 946 | 0.82 | 0.84 | 94 | empty |
| 2 | 210 | 0.68 | 0.85 | 30 | empty |
| 3 | 212 | 0.63 | 0.83 | 41 | MG, BEF, ADP |
| 4 | 59 | 0.59 | 0.91 | 16 | empty |
| 5 | 131 | 0.52 | 0.81 | 25 | empty |
Compared structures
- 5VHC · DHX36 with an N-terminal truncation bound to ADP-BeF3 · the same entry in another collection · chain D against D, TM-score 1.00
- Q05B79 · AlphaFold monomer V2.0 prediction for ATP-dependent DNA/RNA helicase DHX36 (Q05B79) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 Q05B79
- Elsewhere: RCSB PDB 5VHC · PDBe 5VHC · UniProt Q05B79
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