MolNFT v1 · #108470 · protein
Crystal structure of the yeast dead-box splicing factor PRP28 at 2.54 ångströms resolution
4W7S · Pre-mRNA-splicing ATP-dependent RNA helicase PRP28: “Crystal structure of the yeast dead-box splicing factor PRP28 at 2.54 ångströms resolution”. X-ray diffraction, 2 ligands (ANP, MG), 8 pockets (best druggability 0.67). MolNFT v1…
- PDB
- 4W7S
- Type
- protein
- Length
- 903 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pre-mRNA-splicing ATP-dependent RNA helicase PRP28
- EC
- 3.6.4.13
- UniProt
- P23394
- Ligands
- ANP, MG
- Pockets
- 8 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pre-mRNA-splicing ATP-dependent RNA helicase PRP28 (EC 3.6.4.13) | protein | 455 | 42% helix, 14% strand | P23394 |
| B | Pre-mRNA-splicing ATP-dependent RNA helicase PRP28 (EC 3.6.4.13) | protein | 448 | 42% helix, 15% strand | P23394 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains B
- MG · Magnesium ion · metal · 2 copies · chains B
- P6G · Hexaethylene glycol · additive · 8 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 232 | 0.67 | 0.84 | 29 | empty |
| 2 | 628 | 0.67 | 0.77 | 54 | empty |
| 3 | 292 | 0.56 | 0.76 | 40 | empty |
| 4 | 55 | 0.48 | 0.85 | 19 | empty |
| 5 | 75 | 0.47 | 0.82 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1023 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 4W7S · Crystal structure of the yeast DEAD-box splicing factor Prp28 at 2.54 Angstroms resolution · the same entry in another collection · chain A against A, TM-score 1.00
- P23394 · AlphaFold monomer V2.0 prediction for pre-mRNA-splicing ATP-dependent RNA helicase PRP28… · a predicted model of the same protein · chain B against A, TM-score 0.66
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 P23394
- Elsewhere: RCSB PDB 4W7S · PDBe 4W7S · UniProt P23394
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