Crystal structure of Pseudomonas putida methionine gamma-lyase Q349S mutant with L-homocysteine intermediates

Structure

x-ray diffraction · resolution 2.25 · 2 distinct chains · 42% helix, 16% strand (DSSP).

Ligands and binding sites

• 7XF · (2~{S})-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]-4-sulfanyl-butanoic acid · ligand · 2 copies · chains A, B, C, D
• HCS · 2-amino-4-mercapto-butyric acid · ligand · chains C, D

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

Pockets

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

Interfaces

6 interfaces between chains.

• A–B · 2682 Ų buried · 43 hydrogen bonds · protein-protein
• C–D · 2669 Ų buried · 43 hydrogen bonds · protein-protein
• B–C · 1591 Ų buried · 24 hydrogen bonds · protein-protein
• A–D · 1559 Ų buried · 21 hydrogen bonds · protein-protein
• B–D · 752 Ų buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified, 1 covalent (cofactor, covalent ligand).

Compared structures

• 7F1V · Crystal structure of pseudomonas putida methionine gamma-lyase Q349S mutant with… · the same entry in another collection · chain A against A, TM-score 1.00
• P13254 · AlphaFold monomer V2.0 prediction for L-methionine gamma-lyase (P13254) · a predicted model of the same protein · chain B 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 P13254
• Elsewhere: RCSB PDB 7F1V · PDBe 7F1V · UniProt P13254