Research workbench
Crystal structure of budding yeast CDC14P (C283S) bound to a SWI6P phosphopeptide
Analyse Crystal structure of budding yeast CDC14P (C283S) bound to a SWI6P… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XW5
- Type
- protein
- Length
- 734 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein phosphatase CDC14; Regulatory protein SWI6
- EC
- 3.1.3.48
- UniProt
- Q00684, P09959
- Ligands
- SO4
- Pockets
- 10 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein phosphatase CDC14 (EC 3.1.3.48) | protein | 362 | 42% helix, 15% strand | Q00684 |
| B | Tyrosine-protein phosphatase CDC14 (EC 3.1.3.48) | protein | 364 | 42% helix, 14% strand | Q00684 |
| C | Regulatory protein SWI6 | protein | 8 | 0% helix, 0% strand | P09959 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 182 | 0.83 | 0.97 | 35 | empty |
| 2 | 194 | 0.57 | 0.80 | 24 | empty |
| 3 | 178 | 0.56 | 0.80 | 21 | empty |
| 4 | 147 | 0.52 | 0.80 | 22 | empty |
| 5 | 97 | 0.47 | 0.81 | 22 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1775 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 622 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 5XW5 · Crystal structure of budding yeast Cdc14p (C283S) bound to a Swi6p phosphopeptide · the same entry in another collection · chain A against A, TM-score 1.00
- Q00684 · AlphaFold monomer V2.0 prediction for tyrosine-protein phosphatase CDC14 (Q00684) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P09959 · AlphaFold monomer V2.0 prediction for regulatory protein SWI6 (P09959) · a predicted model of the same protein · chain C against A, TM-score 0.51
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 Q00684
- Every structure of UniProt P09959
- Elsewhere: RCSB PDB 5XW5 · PDBe 5XW5 · UniProt Q00684 · UniProt P09959
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.