Crystal structure of N-terminally tagged ubid from E. COLI reconstituted with prfmn cofactor

Structure

x-ray diffraction · 3 distinct chains · 30% helix, 28% strand (DSSP).

Ligands and binding sites

• 7D9 · (16~{R})-11,12,14,14-tetramethyl-3,5-bis(oxidanylidene)-8-[(2~{S},3~{S},4~{R})-2,3,4-tris(oxidanyl)-5-phosphonooxy-pentyl]-1,4,6,8-tetrazatetracyclo[7.7.1.0^{2,7}.0^{13,17}]heptadeca-2(7),9(17),10,12-tetraene-16-sulfonic acid · ligand · 3 copies · chains A, B, C
• MN · Manganese (II) ion · metal · 3 copies · chains A, B, C
• NA · Sodium ion · metal · 3 copies · chains A, B, C

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

Pockets

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

Interfaces

2 interfaces between chains.

• A–B · 4299 Ų buried · 65 hydrogen bonds · protein-protein
• A–C · 1263 Ų buried · 12 hydrogen bonds · protein-protein

Compared structures

• 5M1E · Crystal structure of N-terminally tagged UbiD from E. coli reconstituted with prFMN… · the same entry in another collection · chain A against A, TM-score 1.00
• P0AAB5 · AlphaFold monomer V2.0 prediction for 3-octaprenyl-4-hydroxybenzoate carboxy-lyase… · a predicted model of the same protein · chain C 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 P0AAB5
• Elsewhere: RCSB PDB 5M1E · PDBe 5M1E · UniProt P0AAB5