MolNFT v1 · #123612 · protein
Crystal structure of the PRP43P deah-box RNA helicase in complex with cdp
5JPT · Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43: “Crystal structure of the PRP43P deah-box RNA helicase in complex with cdp”. X-ray diffraction, 3 ligands (CDP, MG, NI), 20 pockets (best druggability 0.81). MolNFT v1…
- PDB
- 5JPT
- Type
- protein
- Length
- 1,486 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43
- EC
- 3.6.4.13
- UniProt
- P53131
- Ligands
- CDP, MG, NI
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 (EC 3.6.4.13) | protein | 745 | 43% helix, 17% strand | P53131 |
| B | Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 (EC 3.6.4.13) | protein | 741 | 42% helix, 16% strand | P53131 |
Ligands and binding sites
- CDP · Cytidine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- NI · Nickel (II) ion · metal · chains A
- GOL · Glycerol · additive · chains A
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1003 | 0.81 | 0.82 | 72 | empty |
| 2 | 792 | 0.81 | 0.84 | 86 | empty |
| 3 | 451 | 0.76 | 0.85 | 58 | empty |
| 4 | 258 | 0.73 | 0.87 | 30 | CDP, MG |
| 5 | 385 | 0.70 | 0.82 | 43 | CDP, MG |
Interfaces
1 interface between chains.
- A–B · 895 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 5JPT · Crystal structure of the PRP43P deah-box RNA helicase in complex with cdp · the same entry in another collection · chain A against A, TM-score 1.00
- P53131 · AlphaFold monomer V2.0 prediction for pre-mRNA-splicing factor ATP- dependent RNA… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P53131
- Elsewhere: RCSB PDB 5JPT · PDBe 5JPT · UniProt P53131
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