MolNFT v1 · #59407 · protein + RNA
PUF4 T650C/C724R mutant bound to COX17 RNA 3' utr recognition sequence
3BX3 · COX17 RNA target sequence: “PUF4 T650C/C724R mutant bound to COX17 RNA 3' utr recognition sequence”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.57). MolNFT v1 #59407 on GenesisL1: 3D structure, binding sites…
- PDB
- 3BX3
- Type
- protein + RNA
- Length
- 641 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- COX17 RNA target sequence; Protein PUF4
- UniProt
- P25339
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | COX17 RNA target sequence | rna | 8 | — | — |
| A | Protein PUF4 | protein | 325 | 75% helix, 0% strand | P25339 |
| B | Protein PUF4 | protein | 300 | 77% helix, 0% strand | P25339 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 351 | 0.57 | 0.75 | 41 | SO4 |
| 2 | 80 | 0.51 | 0.84 | 15 | SO4 |
| 3 | 76 | 0.48 | 0.83 | 15 | empty |
| 4 | 175 | 0.44 | 0.74 | 26 | SO4 |
| 5 | 76 | 0.40 | 0.78 | 16 | empty |
Interfaces
3 interfaces between chains.
- C–A · 1338 Ų buried · 33 hydrogen bonds · protein-nucleic
- D–B · 1252 Ų buried · 28 hydrogen bonds · protein-nucleic
- A–B · 457 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 3BX3 · Puf4 T650C/C724R Mutant bound to Cox17 RNA 3' UTR recognition sequence · the same entry in another collection · chain C against C, TM-score 1.00
- P25339 · AlphaFold monomer V2.0 prediction for pumilio homology domain family member 4 (P25339) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P25339
- Elsewhere: RCSB PDB 3BX3 · PDBe 3BX3 · UniProt P25339
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