Research workbench
A specific and modular binding code for cytosine recognition in puf domains
Analyse A specific and modular binding code for cytosine recognition in puf domains in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YJY
- Type
- protein + RNA
- Length
- 698 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pumilio homolog 1; 5'-R(*AP*UP*UP*GP*CP*AP*UP*AP*UP*AP)-3'
- UniProt
- Q14671
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 73% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pumilio homolog 1 | protein | 337 | 72% helix, 1% strand | Q14671 |
| B | Pumilio homolog 1 | protein | 341 | 73% helix, 1% strand | Q14671 |
| C, D | 5'-R(*AP*UP*UP*GP*CP*AP*UP*AP*UP*AP)-3' | rna | 10 | — | — |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 254 | 0.62 | 0.81 | 30 | empty |
| 2 | 202 | 0.46 | 0.74 | 22 | empty |
| 3 | 59 | 0.46 | 0.83 | 12 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1307 Ų buried · 43 hydrogen bonds · protein-nucleic
- A–C · 1204 Ų buried · 43 hydrogen bonds · protein-nucleic
- A–B · 271 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2YJY · A specific and modular binding code for cytosine recognition in PUF domains · the same entry in another collection · chain A against A, TM-score 1.00
- Q14671 · AlphaFold monomer V2.0 prediction for pumilio homolog 1 (Q14671) · 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 Q14671
- Elsewhere: RCSB PDB 2YJY · PDBe 2YJY · UniProt Q14671
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