Research workbench
Crystal structure of the PRP43P deah-box RNA helicase in complex with ADP
Analyse Crystal structure of the PRP43P deah-box RNA helicase in complex with ADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XAU
- 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
- 3.6.1.-
- UniProt
- P53131
- Ligands
- ADP, MG, NI
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 (EC 3.6.1.-) | protein | 745 | 45% helix, 17% strand | P53131 |
| B | Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 (EC 3.6.1.-) | protein | 741 | 45% helix, 17% strand | P53131 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- NI · Nickel (II) ion · metal · 2 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
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 | 835 | 0.82 | 0.84 | 100 | ACT |
| 2 | 739 | 0.81 | 0.85 | 65 | empty |
| 3 | 654 | 0.78 | 0.84 | 76 | empty |
| 4 | 358 | 0.73 | 0.85 | 51 | ADP, MG |
| 5 | 336 | 0.70 | 0.84 | 47 | ADP, MG |
Interfaces
1 interface between chains.
- A–B · 808 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 2XAU · Crystal structure of the Prp43p DEAH-box RNA helicase in complex with ADP · 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 B 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 2XAU · PDBe 2XAU · UniProt P53131
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