Co-crystal structure of the saccharomyces cerevisiae histidine phosphotransfer signaling protein YPD1 and the receiver domain of its downstream response regulator SSK1

Structure

x-ray diffraction · 2 distinct chains · 54% helix, 8% strand (DSSP).

Ligands and binding sites

• PO4 · Phosphate ion · ion · 2 copies · chains A, B
• GOL · Glycerol · additive · 3 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 811 Ų buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 modified (engineered).

Compared structures

• 5KBX · Co-crystal structure of the Saccharomyces cerevisiae histidine phosphotransfer signaling… · the same entry in another collection · chain A against A, TM-score 1.00
• Q07688 · AlphaFold monomer V2.0 prediction for phosphorelay intermediate protein YPD1 (Q07688) · a predicted model of the same protein · chain A against A, TM-score 0.99
• Q07084 · AlphaFold monomer V2.0 prediction for osmolarity two-component system protein SSK1… · a predicted model of the same protein · chain B against A, TM-score 0.94

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 Q07688
• Every structure of UniProt Q07084
• Elsewhere: RCSB PDB 5KBX · PDBe 5KBX · UniProt Q07688 · UniProt Q07084