Crystal structure of a 4-domain construct of lgra in the substrate donation state

Structure

x-ray diffraction · 1 distinct chain · 35% helix, 23% strand (DSSP).

Ligands and binding sites

• JQG · (2~{R})-~{N}-[3-[2-[[(2~{S})-2-formamido-3-methyl-butanoyl]amino]ethylamino]-3-oxidanylidene-propyl]-3, 3-dimethyl-2-oxidanyl-4-[oxidanyl-bis(oxidanylidene)-$L^{6}-phosphanyl]oxy-butanamide · ligand · chains A
• FON · N-{[4-({[(6R)-2-amino-5-formyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid · ligand · chains A
• APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · chains A
• VAL · Valine · ligand · chains A
• MG · Magnesium ion · metal · chains A
• PO4 · Phosphate ion · ion · chains A

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

Pockets

12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

• 6MFW · Crystal structure of a 4-domain construct of LgrA in the substrate donation state · the same entry in another collection · chain A against A, TM-score 1.00
• Q70LM7 · AlphaFold monomer V2.0 prediction for linear gramicidin synthase subunit a (Q70LM7) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q70LM7
• Elsewhere: RCSB PDB 6MFW · PDBe 6MFW · UniProt Q70LM7