MolNFT v1 · #101124 · protein
Structure of the spliceosomal dead-box protein PRP28
4NHO · Probable ATP-dependent RNA helicase DDX23: “Structure of the spliceosomal dead-box protein PRP28”. X-ray diffraction, 2 ligands (HG, SO4), 5 pockets (best druggability 0.59). MolNFT v1 #101124 on GenesisL1: 3D structure, binding…
- PDB
- 4NHO
- Type
- protein
- Length
- 443 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable ATP-dependent RNA helicase DDX23
- EC
- 3.6.4.13
- UniProt
- Q9BUQ8
- Ligands
- HG, SO4
- Pockets
- 5 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable ATP-dependent RNA helicase DDX23 (EC 3.6.4.13) | protein | 443 | 47% helix, 14% strand | Q9BUQ8 |
Ligands and binding sites
- HG · Mercury (II) ion · metal · chains A
- SO4 · Sulfate ion · ion · 5 copies · chains A
- GOL · Glycerol · additive · 2 copies · chains A
- CXS · 3-cyclohexyl-1-propylsulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 433 | 0.59 | 0.75 | 50 | SO4 |
| 2 | 99 | 0.52 | 0.82 | 16 | empty |
| 3 | 141 | 0.42 | 0.74 | 24 | empty |
| 4 | 65 | 0.36 | 0.78 | 17 | empty |
| 5 | 52 | 0.29 | 0.75 | 21 | empty |
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 4NHO · Structure of the spliceosomal DEAD-box protein Prp28 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9BUQ8 · AlphaFold monomer V2.0 prediction for probable ATP-dependent RNA helicase DDX23 (Q9BUQ8) · a predicted model of the same protein · chain A against A, TM-score 0.64
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 Q9BUQ8
- Elsewhere: RCSB PDB 4NHO · PDBe 4NHO · UniProt Q9BUQ8
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