Crystal structure of pseudomonas putida methionine gamma-lyase C116H mutant with L-homocysteine intermediates.

Structure

x-ray diffraction · 3 distinct chains · 44% helix, 16% strand (DSSP).

Ligands and binding sites

• HCS · 2-amino-4-mercapto-butyric acid · ligand · 2 copies · chains A, B, C, D
• 4LM · (2E)-2-{[(1E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}but-2-enoic acid · ligand · chains A, B
• 7XF · (2~{S})-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]-4-sulfanyl-butanoic acid · ligand · chains C, D
• H2S · Hydrosulfuric acid · ion · chains A, B

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

6 interfaces between chains.

• A–B · 2711 Ų buried · 46 hydrogen bonds · protein-protein
• C–D · 2690 Ų buried · 50 hydrogen bonds · protein-protein
• B–D · 1590 Ų buried · 24 hydrogen bonds · protein-protein
• A–C · 1565 Ų buried · 22 hydrogen bonds · protein-protein
• B–C · 760 Ų buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (cofactor).

Compared structures

• 5X30 · Crystal structure of Pseudomonas putida methionine gamma-lyase C116H mutant with… · the same entry in another collection · chain D against D, TM-score 1.00
• P13254 · AlphaFold monomer V2.0 prediction for L-methionine gamma-lyase (P13254) · a predicted model of the same protein · chain C 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 5X30 · PDBe 5X30 · UniProt P13254