Crystal structure of L147A/I351A variant of S-adenosylmethionine synthetase from methanocaldococcus jannaschii in complex with onb-SAM (2-nitro benzyme S-adenosyl-methionine)

Structure

x-ray diffraction · 2 distinct chains · 35% helix, 29% strand (DSSP).

Ligands and binding sites

• 3PO · Triphosphate · ligand · 2 copies · chains A, C
• EU9 · [(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl) oxolan-2-yl]methyl-[(3R)-3-azanyl-4-oxidanyl-4-oxidanylidene-butyl]-[(2-nitrophenyl)methyl]sulfanium · ligand · chains A, C
• MG · Magnesium ion · metal · 3 copies · chains A, C

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

Pockets

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

Interfaces

1 interface between chains.

• A–C · 2747 Ų buried · 43 hydrogen bonds · protein-protein

Compared structures

• 7P84 · Crystal structure of L147A/I351A variant of S-adenosylmethionine synthetase from… · the same entry in another collection · chain A against A, TM-score 1.00
• Q58605 · AlphaFold monomer V2.0 prediction for S-adenosylmethionine synthase (Q58605) · a predicted model of the same protein · chain C 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 Q58605
• Elsewhere: RCSB PDB 7P84 · PDBe 7P84 · UniProt Q58605