Research workbench
Crystal structure of RNA splicing effector PRP5 in complex with ADP
Analyse Crystal structure of RNA splicing effector PRP5 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
- 4LJY
- Type
- protein
- Length
- 451 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pre-mRNA-processing ATP-dependent RNA helicase PRP5
- EC
- 3.6.4.13
- UniProt
- P21372
- Ligands
- ADP, MG
- Pockets
- 4 · best druggability 0.51
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pre-mRNA-processing ATP-dependent RNA helicase PRP5 (EC 3.6.4.13) | protein | 451 | 47% helix, 15% strand | P21372 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 136 | 0.51 | 0.79 | 22 | empty |
| 2 | 158 | 0.43 | 0.75 | 41 | empty |
| 3 | 95 | 0.37 | 0.75 | 15 | empty |
| 4 | 86 | 0.37 | 0.76 | 16 | ADP, MG |
Modifications
Observed in the structure: 13 modified (engineered).
Compared structures
- 4LJY · Crystal structure of RNA splicing effector Prp5 in complex with ADP · the same entry in another collection · chain A against A, TM-score 1.00
- P21372 · AlphaFold monomer V2.0 prediction for pre-mRNA-processing ATP- dependent RNA helicase… · a predicted model of the same protein · chain A against A, TM-score 0.60
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 P21372
- Elsewhere: RCSB PDB 4LJY · PDBe 4LJY · UniProt P21372
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