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

Structure

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

Ligands and binding sites

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

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

Pockets

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

Interfaces

6 interfaces between chains.

• C–D · 2603 Ų buried · 53 hydrogen bonds · protein-protein
• A–B · 2591 Ų buried · 47 hydrogen bonds · protein-protein
• A–C · 1519 Ų buried · 21 hydrogen bonds · protein-protein
• B–D · 1517 Ų buried · 22 hydrogen bonds · protein-protein
• B–C · 952 Ų buried · 20 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 modified (cofactor).

Compared structures

• 4IYO · Crystal structure of cystathionine gamma lyase from Xanthomonas oryzae pv. oryzae… · the same entry in another collection · chain B against B, 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 4IYO · PDBe 4IYO · UniProt Q5H4T8