Research workbench
Crystal structure of yeast PUF4P RNA binding domain in complex with ho-4BE mutant RNA
Analyse Crystal structure of yeast PUF4P RNA binding domain in complex with ho-4BE… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DZS
- Type
- protein + RNA
- Length
- 665 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pumilio homology domain family member 4; 5'-R(*UP*GP*UP*AP*UP*CP*AP*UP*A)-3'
- UniProt
- P25339
- Pockets
- 6 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pumilio homology domain family member 4 | protein | 328 | 74% helix, 0% strand | P25339 |
| B | Pumilio homology domain family member 4 | protein | 319 | 74% helix, 0% strand | P25339 |
| C, D | 5'-R(*UP*GP*UP*AP*UP*CP*AP*UP*A)-3' | rna | 9 | — | — |
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 | 350 | 0.58 | 0.76 | 40 | empty |
| 2 | 84 | 0.53 | 0.84 | 14 | empty |
| 3 | 230 | 0.50 | 0.75 | 31 | empty |
| 4 | 101 | 0.48 | 0.81 | 16 | empty |
| 5 | 68 | 0.34 | 0.76 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1240 Ų buried · 33 hydrogen bonds · protein-nucleic
- B–D · 1233 Ų buried · 39 hydrogen bonds · protein-nucleic
- A–B · 508 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4DZS · Crystal structure of yeast Puf4p RNA binding domain in complex with HO-4BE mutant RNA · 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 B against A, TM-score 0.98
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 4DZS · PDBe 4DZS · UniProt P25339
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