Crystal structure of the (sr) calcium ATPase E2-vanadate complex bound to thapsigargin and tnp-ATP

Structure

x-ray diffraction · 1 distinct chain · 47% helix, 16% strand (DSSP).

Ligands and binding sites

• ACE · Acetyl group · ligand · 2 copies · chains A, B
• TG1 · Octanoic acid [3S-[3alpha, 3abeta, 4alpha, 6beta, 6abeta, 7beta, 8alpha(z), 9balpha]]-6-(acetyloxy)-2,3, -3A,4,5,6,6A,7,8,9B-decahydro-3,3A-dihydroxy-3,6,9-trimethyl-8-[(2-methyl-1-oxo-2-butenyl)oxy]-2-oxo-4-(1-oxobutoxy)-azuleno[4,5-b]furan-7-yl ester · ligand · 2 copies · chains A, B
• VN4 · oxido(dioxo)vanadium · ligand · 2 copies · chains A, B
• 128 · Spiro(2,4,6-trinitrobenzene[1,2a]-2O',3O'-methylene-adenine-triphosphate · ligand · 2 copies · chains A, B
• MG · Magnesium ion · metal · 4 copies · chains A, B
• K · Potassium ion · metal · 2 copies · chains A, B
• CL · Chloride ion · ion · 2 copies · chains A, B

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

Pockets

20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 436 Ų buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

• P04191 · AlphaFold monomer V2.0 prediction for SARCOPLASMIC/ENDOPLASMIC reticulum calcium ATPase 1… · a predicted model of the same protein · chain B against A, TM-score 0.91

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 P04191
• Elsewhere: RCSB PDB 5A3S · PDBe 5A3S · UniProt P04191