Crystal structure of GENB1 from micromonospora echinospora in complex with ji-20A and plp (external aldimine)

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 16% strand (DSSP).

Ligands and binding sites

• PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
• JIA · (2~{R},3~{R},4~{R},5~{R})-2-[(1~{S},2~{S},3~{R},4~{S}, 6~{R})-3-[(2~{R},3~{R},4~{R},5~{S},6~{R})-6-(aminomethyl)-3-azanyl-4,5-bis(oxidanyl)oxan-2-yl]oxy-4,6-bis(azanyl)-2-oxidanyl-cyclohexyl]oxy-5-methyl-4-(methylamino)oxane-3,5-diol · ligand · 2 copies · chains A, B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 3433 Ų buried · 59 hydrogen bonds · protein-protein

Compared structures

• 5Z8A · Crystal structure of GenB1 from Micromonospora echinospora in complex with JI-20A and PLP… · the same entry in another collection · chain A against A, TM-score 1.00

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 Q70KD9
• Elsewhere: RCSB PDB 5Z8A · PDBe 5Z8A · UniProt Q70KD9