Research workbench
PUF4 RNA binding domain bound to ho endonuclease RNA 3' utr recognition sequence
Analyse PUF4 RNA binding domain bound to ho endonuclease RNA 3' utr recognition sequence in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BX2
- Type
- protein + RNA
- Length
- 669 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein PUF4; Ho endonuclease 3' utr binding sequence
- UniProt
- P25339
- Ligands
- NA, SO4
- Pockets
- 6 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein PUF4 | protein | 328 | 79% helix, 0% strand | P25339 |
| B | Protein PUF4 | protein | 323 | 79% helix, 0% strand | P25339 |
| C, D | Ho endonuclease 3' utr binding sequence | rna | 9 | — | — |
Ligands and binding sites
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 | 300 | 0.57 | 0.76 | 37 | SO4 |
| 2 | 82 | 0.52 | 0.84 | 14 | empty |
| 3 | 231 | 0.49 | 0.75 | 35 | empty |
| 4 | 72 | 0.48 | 0.83 | 15 | empty |
| 5 | 101 | 0.33 | 0.73 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1259 Ų buried · 34 hydrogen bonds · protein-nucleic
- B–D · 1250 Ų buried · 32 hydrogen bonds · protein-nucleic
- A–B · 552 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 3BX2 · Puf4 RNA binding domain bound to HO endonuclease RNA 3' UTR recognition sequence · the same entry in another collection · chain A against A, 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 A 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 3BX2 · PDBe 3BX2 · UniProt P25339
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