Crystal structure of an engineered tyca variant in complex with an O- propargyl-beta-tyr-AMP analog

Structure

x-ray diffraction · 2 distinct chains · 31% helix, 26% strand (DSSP).

Ligands and binding sites

• 8Q2 · [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[(3~{S})-3-azanyl-3-(4-prop-2-ynoxyphenyl)propanoyl]sulfamate · ligand · 2 copies · chains A, B
• SO4 · Sulfate ion · ion · 2 copies · chains A, B
• BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · chains B

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

Pockets

9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 392 Ų buried · 9 hydrogen bonds · protein-protein

Compared structures

• 5N81 · Crystal structure of an engineered TycA variant in complex with an… · the same entry in another collection · chain A against A, TM-score 1.00
• P09095 · AlphaFold monomer V2.0 prediction for tyrocidine synthase 1 (P09095) · a predicted model of the same protein · chain B 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 P09095
• Elsewhere: RCSB PDB 5N81 · PDBe 5N81 · UniProt P09095