Crystal structure of bradyrhizobium japonicum GLYCINE:[CARRIER protein] ligase complexed with cognate carrier protein and ATP

Structure

x-ray diffraction · 4 distinct chains · 40% helix, 23% strand (DSSP).

Ligands and binding sites

• ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
• PNS · 4'-phosphopantetheine · ligand · 2 copies · chains A, C, B, D
• ZN · Zinc ion · metal · 2 copies · chains A, B
• MG · Magnesium ion · metal · 2 copies · chains A, B
• SO4 · Sulfate ion · ion · chains B
• ACT · Acetate ion · additive · chains B

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

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Interfaces

4 interfaces between chains.

• A–B · 2499 Ų buried · 20 hydrogen bonds · protein-protein
• B–D · 670 Ų buried · 4 hydrogen bonds · protein-protein
• A–C · 576 Ų buried · 4 hydrogen bonds · protein-protein
• A–D · 12 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 cofactor (phosphopantetheinylation).

Compared structures

• 4H2U · Crystal structure of Bradyrhizobium japonicum glycine:[carrier protein] ligase complexed… · the same entry in another collection · chain D against D, TM-score 1.00
• Q89VT8 · AlphaFold monomer V2.0 prediction for amino acid--[acyl-carrier- protein] ligase 1… · a predicted model of the same protein · chain A against A, TM-score 1.00
• Q89VT6 · AlphaFold monomer V2.0 prediction for aminoacyl carrier protein 1 (Q89VT6) · a predicted model of the same protein · chain D against A, TM-score 0.97

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 Q89VT8
• Every structure of UniProt Q89VT6
• Elsewhere: RCSB PDB 4H2U · PDBe 4H2U · UniProt Q89VT8 · UniProt Q89VT6