Complex structure of bacillus subtilis ribg: the deamination process in riboflavin biosynthesis

Structure

x-ray diffraction · 2 distinct chains · 30% helix, 25% strand (DSSP).

Ligands and binding sites

• AI9 · [(2R,3S,4S,5E)-5-[[5-azanyl-2,4-bis(oxidanylidene)-1H-pyrimidin-6-yl]imino]-2,3,4-tris(oxidanyl)pentyl] dihydrogen phosphate · ligand · 4 copies · chains A, B, C, D
• AOF · N-(5-amino-2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl)-5-O-phosphono-beta-D-ribofuranosylamine · ligand · 3 copies · chains B, C, D
• ZN · Zinc ion · metal · 4 copies · chains A, B, C, D

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

Pockets

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

Interfaces

4 interfaces between chains.

• B–D · 2035 Ų buried · 20 hydrogen bonds · protein-protein
• A–C · 1993 Ų buried · 22 hydrogen bonds · protein-protein
• A–B · 1063 Ų buried · 13 hydrogen bonds · protein-protein
• C–D · 991 Ų buried · 15 hydrogen bonds · protein-protein

Compared structures

• 4G3M · Complex Structure of Bacillus subtilis RibG: The Deamination Process in Riboflavin… · the same entry in another collection · chain A against A, TM-score 1.00
• P17618 · AlphaFold monomer V2.0 prediction for riboflavin biosynthesis protein ribd (P17618) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 P17618
• Elsewhere: RCSB PDB 4G3M · PDBe 4G3M · UniProt P17618