Crystal structure of B1 immunoglobulin-binding domain of streptococcal protein G (T16F, T18A, V21H, T25H, K28Y, V29I, K31R, Q32A, Y33L, N35K, D36A, N37Q)

Structure

x-ray diffraction · 1 distinct chain · 30% helix, 43% strand (DSSP).

Ligands and binding sites

• DPO · Diphosphate · ligand · chains A, B
• ZN · Zinc ion · metal · 4 copies · chains A, B
• NA · Sodium ion · metal · 4 copies · chains A, B, C, D
• PO4 · Phosphate ion · ion · 2 copies · chains A, B
• CL · Chloride ion · ion · chains A
• ACT · Acetate ion · additive · 8 copies · chains A, B, C, D

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

3 interfaces between chains.

• B–C · 535 Ų buried · 10 hydrogen bonds · protein-protein
• A–B · 304 Ų buried · 5 hydrogen bonds · protein-protein
• C–D · 300 Ų buried · 8 hydrogen bonds · protein-protein

Compared structures

• 6NL7 · Crystal structure of B1 immunoglobulin-binding domain of Streptococcal Protein G (T16F… · the same entry in another collection · chain A against A, TM-score 1.00
• P19909 · AlphaFold monomer V2.0 prediction for immunoglobulin G-binding protein G (P19909) · a predicted model of the same protein · chain A 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 P19909
• Elsewhere: RCSB PDB 6NL7 · PDBe 6NL7 · UniProt P19909