Methylmalonyl-CoA decarboxylase in complex with 2-nitronate-propionyl- OXA(DETHIA)-CoA

Structure

x-ray diffraction · 1 distinct chain · 46% helix, 17% strand (DSSP).

Ligands and binding sites

• KGA · [1-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethoxy]-1-oxidanylidene-propan-2-ylidene]-bis(oxidanidyl)azanium · ligand · 9 copies · chains A, B, C, D, E, F
• KG7 · (2E)-2-(hydroxyimino)propanoic acid · ligand · chains F
• NI · Nickel (II) ion · metal · 3 copies · chains A, B, C, D, E, F
• K · Potassium ion · metal · chains C
• IMD · Imidazole · additive · 3 copies · chains A, B, C, D, F
• PG4 · Tetraethylene glycol · additive · chains C

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

Pockets

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Interfaces

15 interfaces between chains.

• B–C · 1733 Ų buried · 27 hydrogen bonds · protein-protein
• A–C · 1733 Ų buried · 26 hydrogen bonds · protein-protein
• D–F · 1732 Ų buried · 25 hydrogen bonds · protein-protein
• A–B · 1714 Ų buried · 26 hydrogen bonds · protein-protein
• E–F · 1707 Ų buried · 25 hydrogen bonds · protein-protein

Compared structures

• 6N93 · Methylmalonyl-CoA decarboxylase in complex with 2-nitronate-propionyl-oxa(dethia)-CoA · the same entry in another collection · chain C against C, TM-score 1.00
• P52045 · AlphaFold monomer V2.0 prediction for methylmalonyl-CoA decarboxylase (P52045) · a predicted model of the same protein · 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 P52045
• Elsewhere: RCSB PDB 6N93 · PDBe 6N93 · UniProt P52045