Research workbench
Crystal structure of the PRP43-ADP-BEF3-U7-RNA complex
Analyse Crystal structure of the PRP43-ADP-BEF3-U7-RNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LTA
- Type
- protein + RNA
- Length
- 705 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; RNA…
- EC
- 3.6.4.13
- UniProt
- G0RY84
- Ligands
- ADP, BEF, MG
- Pockets
- 9 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 18% 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 | 698 | 42% helix, 18% strand | G0RY84 |
| E | RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*U)-3') | rna | 7 | — | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- BEF · Beryllium trifluoride ion · ligand · chains A
- MG · Magnesium ion · metal · chains A
- CAC · Cacodylate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1164 | 0.86 | 0.87 | 101 | empty |
| 2 | 204 | 0.67 | 0.85 | 27 | empty |
| 3 | 277 | 0.64 | 0.81 | 37 | ADP, MG, BEF |
| 4 | 296 | 0.60 | 0.79 | 38 | empty |
| 5 | 143 | 0.39 | 0.74 | 24 | empty |
Interfaces
1 interface between chains.
- A–E · 1126 Ų buried · 18 hydrogen bonds · protein-nucleic
Compared structures
- 5LTA · Crystal structure of the Prp43-ADP-BeF3-U7-RNA complex · the same entry in another collection · chain A against A, TM-score 1.00
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 G0RY84
- Elsewhere: RCSB PDB 5LTA · PDBe 5LTA · UniProt G0RY84
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