MolNFT v1 · #111144 · protein + RNA
Yeast PRP3 (296-469) in complex with fragment of U4/U6 di-snrna
4YHW · U4/U6 small nuclear ribonucleoprotein PRP3: “Yeast PRP3 (296-469) in complex with fragment of U4/U6 di-snrna”. X-ray diffraction, 8 pockets (best druggability 0.55). MolNFT v1 #111144 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4YHW
- Type
- protein + RNA
- Length
- 354 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- U4/U6 small nuclear ribonucleoprotein PRP3; U4 snrna fragment; U6 snrna fragment
- UniProt
- Q03338
- Pockets
- 8 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | U4/U6 small nuclear ribonucleoprotein PRP3 | protein | 133 | 30% helix, 31% strand | Q03338 |
| C, D | U4 snrna fragment | rna | 17 | — | — |
| E, F | U6 snrna fragment | rna | 27 | — | — |
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 476 | 0.55 | 0.73 | 30 | empty |
| 2 | 457 | 0.53 | 0.73 | 25 | empty |
| 3 | 105 | 0.49 | 0.80 | 19 | empty |
| 4 | 82 | 0.45 | 0.81 | 23 | empty |
| 5 | 137 | 0.44 | 0.77 | 11 | empty |
Interfaces
5 interfaces between chains.
- A–E · 982 Ų buried · 26 hydrogen bonds · protein-nucleic
- C–E · 832 Ų buried · 53 hydrogen bonds · nucleic-nucleic
- B–F · 831 Ų buried · 21 hydrogen bonds · protein-nucleic
- D–F · 827 Ų buried · 74 hydrogen bonds · nucleic-nucleic
- A–B · 604 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 4YHW · Yeast Prp3 (296-469) in complex with fragment of U4/U6 di-snRNA · the same entry in another collection · chain B against B, TM-score 1.00
- Q03338 · AlphaFold monomer V2.0 prediction for U4/U6 small nuclear ribonucleoprotein PRP3 (Q03338) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q03338
- Elsewhere: RCSB PDB 4YHW · PDBe 4YHW · UniProt Q03338
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