Crystal structure of dipeptide epimerase from methylococcus capsulatus complexed with mg and dipeptide L-arg-D-lys

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 23% strand (DSSP).

Ligands and binding sites

• MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, E
• SO4 · Sulfate ion · ion · 25 copies · chains A, C, B, D, E
• 1PE · Pentaethylene glycol · additive · 4 copies · chains A, B, C, D, E

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

Pockets

17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Interfaces

6 interfaces between chains.

• D–E · 1205 Ų buried · 7 hydrogen bonds · protein-protein
• A–C · 1192 Ų buried · 7 hydrogen bonds · protein-protein
• C–D · 411 Ų buried · 4 hydrogen bonds · protein-protein
• A–B · 230 Ų buried · 4 hydrogen bonds · protein-protein
• B–C · 199 Ų buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 d-amino (D-amino acid).

Compared structures

• 3RIT · Crystal structure of Dipeptide Epimerase from Methylococcus capsulatus complexed with Mg… · the same entry in another collection · chain A against A, TM-score 1.00
• Q607C7 · AlphaFold monomer V2.0 prediction for L-lys-D/L-arg epimerase (Q607C7) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q607C7
• Elsewhere: RCSB PDB 3RIT · PDBe 3RIT · UniProt Q607C7