Crystal structure of pltf trapped with pltl using a proline adenosine vinylsulfonamide inhibitor

Structure

x-ray diffraction · 2 distinct chains · 35% helix, 21% strand (DSSP).

Ligands and binding sites

• I5M · 5'-deoxy-5'-({(2S)-2-({2-[(N-{(2R)-4-[(dioxo-lambda~5~-phosphanyl)oxy]-2-hydroxy-3,3-dimethylbutanoyl}-beta-alanyl)amino]ethyl}sulfanyl)-2-[(2S)-pyrrolidin-2-yl]ethanesulfonyl}amino)adenosine · ligand · chains B, E
• FMT · Formic acid · additive · 13 copies · chains B, E
• MLA · Malonic acid · additive · 2 copies · chains B
• TRS · 2-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

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

Interfaces

1 interface between chains.

• B–E · 871 Ų buried · 2 hydrogen bonds · protein-protein

Modifications

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

Compared structures

• 6O6E · Crystal structure of PltF trapped with PltL using a proline adenosine vinylsulfonamide… · the same entry in another collection · chain B against B, TM-score 1.00
• Q4KCY5 · AlphaFold monomer V2.0 prediction for L-proline--[L-prolyl-carrier protein] ligase… · a predicted model of the same protein · chain B against A, TM-score 0.95

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 Q4KCY5
• Every structure of UniProt Q4KCZ1
• Elsewhere: RCSB PDB 6O6E · PDBe 6O6E · UniProt Q4KCY5 · UniProt Q4KCZ1