Fully ligated adenylosuccinate synthetase from pyrococcus horikoshii OT3 with GTP, imp and hadacidin

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 20% strand (DSSP).

Ligands and binding sites

• GTP · Guanosine-5'-triphosphate · ligand · 6 copies · chains A, B, C, D, E, F
• IMP · Inosinic acid · ligand · 6 copies · chains A, B, C, D, E, F
• HDA · Hadacidin · ligand · 6 copies · chains A, B, C, D, E, F
• MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F

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

Pockets

18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Interfaces

5 interfaces between chains.

• A–B · 2374 Ų buried · 43 hydrogen bonds · protein-protein
• E–F · 2372 Ų buried · 41 hydrogen bonds · protein-protein
• C–D · 2332 Ų buried · 36 hydrogen bonds · protein-protein
• B–C · 688 Ų buried · 4 hydrogen bonds · protein-protein
• B–E · 189 Ų buried · 1 hydrogen bond · protein-protein

Modifications

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

Compared structures

• 5K7X · Fully ligated Adenylosuccinate Synthetase from Pyrococcus horikoshii OT3 with GTP, IMP… · the same entry in another collection · chain C against C, TM-score 1.00
• O58187 · AlphaFold monomer V2.0 prediction for adenylosuccinate synthetase (O58187) · a predicted model of the same protein · chain A against A, TM-score 1.00

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 O58187
• Elsewhere: RCSB PDB 5K7X · PDBe 5K7X · UniProt O58187