Crystal structure of a glucarate dehydratase related protein, from actinobacillus succinogenes, target efi-502312, with sodium and sulfate bound, ordered loop

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 17% strand (DSSP).

Ligands and binding sites

• NA · Sodium ion · metal · 4 copies · chains A, B, C, D
• SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
• GOL · Glycerol · additive · 7 copies · chains A, D, B, C
• DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · 3 copies · chains B, C, D
• DTU · (2R,3S)-1,4-dimercaptobutane-2,3-diol · additive · chains A

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

Pockets

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

Interfaces

6 interfaces between chains.

• A–B · 1355 Ų buried · 21 hydrogen bonds · protein-protein
• C–D · 1327 Ų buried · 23 hydrogen bonds · protein-protein
• B–D · 712 Ų buried · 24 hydrogen bonds · protein-protein
• A–C · 691 Ų buried · 24 hydrogen bonds · protein-protein
• A–D · 414 Ų buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent (additive adduct).

Compared structures

• 4G8T · Crystal structure of a glucarate dehydratase related protein, from actinobacillus… · the same entry in another collection · chain A 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 A6VQF1
• Elsewhere: RCSB PDB 4G8T · PDBe 4G8T · UniProt A6VQF1