MolNFT v1 · #171954 · protein + RNA
Crystal structure of the deah-box ATPase PRP2 in complex with ADP-BEF3 and ssrna
6ZM2 · Putative mRNA splicing factor: “Crystal structure of the deah-box ATPase PRP2 in complex with ADP-BEF3 and ssrna”. X-ray diffraction, 4 ligands (BEF, ADP, MG), 8 pockets (best druggability 0.87). MolNFT v1 #171954 on GenesisL1: 3D…
- PDB
- 6ZM2
- Type
- protein + RNA
- Length
- 634 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative mRNA splicing factor; RNA (5'-R(P*UP*UP*UP*UP*UP*UP*U)-3')
- UniProt
- G0SEG4
- Ligands
- BEF, ADP, MG, CL
- Pockets
- 8 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative mRNA splicing factor | protein | 627 | 44% helix, 20% strand | G0SEG4 |
| B | RNA (5'-R(P*UP*UP*UP*UP*UP*UP*U)-3') | rna | 7 | — | — |
Ligands and binding sites
- BEF · Beryllium trifluoride ion · ligand · chains A
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · chains A
- POL · N-propanol · additive · 9 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A
- EDO · 1,2-ethanediol · additive · 4 copies · chains A
- PGO · S-1,2-propanediol · additive · 3 copies · chains A
- MPO · 3[N-morpholino]propane sulfonic acid · additive · 2 copies · chains A
- GOL · Glycerol · additive · chains A
- HEZ · Hexane-1,6-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1145 | 0.87 | 0.88 | 106 | PGO, POL, EDO |
| 2 | 106 | 0.67 | 0.91 | 24 | POL |
| 3 | 187 | 0.61 | 0.83 | 31 | BEF, ADP, MG, HEZ |
| 4 | 105 | 0.48 | 0.80 | 15 | empty |
| 5 | 145 | 0.40 | 0.73 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1091 Ų buried · 18 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 6ZM2 · Crystal structure of the DEAH-box ATPase Prp2 in complex with ADP-BeF3 and ssRNA · 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 G0SEG4
- Elsewhere: RCSB PDB 6ZM2 · PDBe 6ZM2 · UniProt G0SEG4
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