Research workbench
Structure of Yeast Frequenin bound to PdtIns 4-kinase
Analyse Structure of Yeast Frequenin bound to PdtIns 4-kinase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2JU0
- Type
- protein
- Length
- 227 residues
- Chains
- 2
- Method
- solution nmr
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- NOT
- Source
- Saccharomyces cerevisiae
- Molecule
- Calcium-binding protein NCS-1; Phosphatidylinositol 4-kinase PIK1
- EC
- 2.7.1.67
- UniProt
- Q06389, P39104
- Ligands
- CA
- Pockets
- 5 · best druggability 0.71
Structure
solution nmr · resolution NOT · 2 distinct chains · 53% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Calcium-binding protein NCS-1 | protein | 175 | 56% helix, 6% strand | Q06389 |
| B | Phosphatidylinositol 4-kinase PIK1 (EC 2.7.1.67) | protein | 52 | 44% helix, 0% strand | P39104 |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 421 | 0.71 | 0.82 | 50 | empty |
| 2 | 115 | 0.49 | 0.80 | 29 | empty |
| 3 | 98 | 0.37 | 0.75 | 16 | empty |
| 4 | 56 | 0.33 | 0.77 | 15 | empty |
| 5 | 55 | 0.32 | 0.76 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 1610 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2JU0 · Structure of yeast frequenin bound to pdtins 4-kinase · the same entry in another collection · chain A against A, TM-score 1.00
- Q06389 · AlphaFold monomer V2.0 prediction for calcium-binding protein ncs-1 (Q06389) · a predicted model of the same protein · chain A against A, TM-score 0.85
- P39104 · AlphaFold monomer V2.0 prediction for phosphatidylinositol 4-kinase PIK1 (P39104) · a predicted model of the same protein · chain B against A, TM-score 0.43
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 Q06389
- Every structure of UniProt P39104
- Elsewhere: RCSB PDB 2JU0 · PDBe 2JU0 · UniProt Q06389 · UniProt P39104
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