Crystal structure of cystathionine gamma lyase (xometc) from xanthomonas oryzae pv. oryzae in complex with E-site serine, a-site external aldimine structure with serine and a-site external aldimine structure with aminoacrylate intermediates

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 17% strand (DSSP).

Ligands and binding sites

• SER · Serine · ligand · 4 copies · chains A, B, C, D
• KOU · (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-serine · ligand · 3 copies · chains A, B, C, D
• PYR · Pyruvic acid · ligand · 2 copies · chains A, B, D
• 0JO · 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid · ligand · chains A, B
• SO4 · Sulfate ion · ion · chains A, B
• GOL · Glycerol · additive · 2 copies · chains A

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

Pockets

20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Interfaces

6 interfaces between chains.

• C–D · 2599 Ų buried · 42 hydrogen bonds · protein-protein
• A–B · 2589 Ų buried · 42 hydrogen bonds · protein-protein
• A–C · 1521 Ų buried · 22 hydrogen bonds · protein-protein
• B–D · 1521 Ų buried · 21 hydrogen bonds · protein-protein
• B–C · 955 Ų buried · 20 hydrogen bonds · protein-protein

Compared structures

• 4IY7 · crystal structure of cystathionine gamma lyase (XometC) from Xanthomonas oryzae pv.… · the same entry in another collection · chain C against C, 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 Q5H4T8
• Elsewhere: RCSB PDB 4IY7 · PDBe 4IY7 · UniProt Q5H4T8