Structure of the effector-binding domain of deoxyribonucleoside regulator deor from bacillus subtilis in complex with deoxyribose-5- phosphate

Structure

x-ray diffraction · 1 distinct chain · 44% helix, 16% strand (DSSP).

Ligands and binding sites

• PED · Pentane-3,4-diol-5-phosphate · ligand · chains A
• NI · Nickel (II) ion · metal · 3 copies · chains A
• CD · Cadmium ion · metal · chains A
• CO · Cobalt (II) ion · metal · chains A
• MG · Magnesium ion · metal · chains A

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

Pockets

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

Modifications

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

Compared structures

• 4OQP · Structure of the effector-binding domain of deoxyribonucleoside regulator DeoR from… · the same entry in another collection · chain A against A, TM-score 1.00
• P39140 · AlphaFold monomer V2.0 prediction for deoxyribonucleoside regulator (P39140) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P39140
• Elsewhere: RCSB PDB 4OQP · PDBe 4OQP · UniProt P39140