Crystal structure of the second tetrahedral intermediates of sgpb at pH 7.3

Structure

x-ray diffraction · 1 distinct chain · 6% helix, 52% strand (DSSP).

Ligands and binding sites

• CL · Chloride ion · ion · 10 copies · chains A, B
• SO4 · Sulfate ion · ion · 5 copies · chains A, B
• EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
• GOL · Glycerol · additive · 4 copies · chains A, B
• ACY · Acetic acid · additive · 3 copies · chains A, B
• EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A, B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 514 Ų buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

• 2QAA · Crystal structure of the second tetrahedral intermediates of SGPB at pH 7.3 · the same entry in another collection · chain A against A, TM-score 1.00
• P00777 · AlphaFold monomer V2.0 prediction for streptogrisin-B (P00777) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P00777
• Elsewhere: RCSB PDB 2QAA · PDBe 2QAA · UniProt P00777