Research workbench
Crystal structure of S. cerevisiae deah-box RNA helicase DHR1, essential for small ribosomal subunit biogenesis
Analyse Crystal structure of S. cerevisiae deah-box RNA helicase DHR1, essential for… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H57
- Type
- protein
- Length
- 795 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable ATP-dependent RNA helicase DHR1
- EC
- 3.6.4.13
- UniProt
- Q04217
- Ligands
- MG, CL
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable ATP-dependent RNA helicase DHR1 (EC 3.6.4.13) | protein | 795 | 40% helix, 18% strand | Q04217 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · 4 copies · chains A
- EDO · 1,2-ethanediol · additive · 14 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 893 | 0.79 | 0.82 | 98 | EDO, CL |
| 2 | 696 | 0.71 | 0.78 | 76 | EDO |
| 3 | 152 | 0.46 | 0.77 | 23 | empty |
| 4 | 100 | 0.40 | 0.76 | 15 | empty |
| 5 | 62 | 0.35 | 0.77 | 15 | empty |
Compared structures
- 6H57 · Crystal structure of S. cerevisiae DEAH-box RNA helicase Dhr1, essential for small… · the same entry in another collection · chain A against A, TM-score 1.00
- Q04217 · AlphaFold monomer V2.0 prediction for probable ATP-dependent RNA helicase DHR1 (Q04217) · a predicted model of the same protein · chain A against A, TM-score 0.82
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 Q04217
- Elsewhere: RCSB PDB 6H57 · PDBe 6H57 · UniProt Q04217
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