MolNFT v1 · #126127 · protein
Crystal structure of the PRP43-ADP-BEF3 complex (in orthorhombic space group)
5LTJ · Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43: “Crystal structure of the PRP43-ADP-BEF3 complex (in orthorhombic space group)”. X-ray diffraction, 5 ligands (ADP, BEF, MG), 7 pockets (best druggability 0.72). MolNFT v1…
- PDB
- 5LTJ
- Type
- protein
- Length
- 703 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43
- UniProt
- G0RY84
- Ligands
- ADP, BEF, MG, CL, SO4
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 | protein | 703 | 45% helix, 18% strand | G0RY84 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- BEF · Beryllium trifluoride ion · ligand · chains A
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · 4 copies · chains A
- SO4 · Sulfate ion · ion · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 7 copies · chains A
- MRD · (4R)-2-methylpentane-2,4-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1035 | 0.72 | 0.76 | 79 | MPD, SO4, CL |
| 2 | 303 | 0.67 | 0.82 | 35 | MPD |
| 3 | 243 | 0.64 | 0.83 | 36 | ADP, BEF, MG |
| 4 | 160 | 0.62 | 0.84 | 33 | empty |
| 5 | 110 | 0.38 | 0.74 | 21 | empty |
Compared structures
- 5LTJ · Crystal structure of the Prp43-ADP-BeF3 complex (in orthorhombic space group) · 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 5LTJ · PDBe 5LTJ · UniProt G0RY84
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