Crystal structure of N-succinylarginine dihydrolase, astb, bound to substrate and product, an enzyme from the arginine catabolic pathway of escherichia COLI

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 20% strand (DSSP).

Ligands and binding sites

• SUG · N~2~-(3-carboxypropanoyl)-L-arginine · ligand · 4 copies · chains A, B, C, D
• K · Potassium ion · metal · 4 copies · chains A, B, 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, 13 with a druggability of 0.5 or more.

Interfaces

5 interfaces between chains.

• A–D · 945 Ų buried · 6 hydrogen bonds · protein-protein
• B–C · 941 Ų buried · 8 hydrogen bonds · protein-protein
• B–D · 472 Ų buried · 6 hydrogen bonds · protein-protein
• C–D · 315 Ų buried · 3 hydrogen bonds · protein-protein
• A–C · 267 Ų buried · 3 hydrogen bonds · protein-protein

Compared structures

• 1YNI · Crystal Structure of N-Succinylarginine Dihydrolase, AstB, bound to Substrate and… · the same entry in another collection · chain D against D, TM-score 1.00
• P76216 · AlphaFold monomer V2.0 prediction for N-succinylarginine dihydrolase (P76216) · 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 P76216
• Elsewhere: RCSB PDB 1YNI · PDBe 1YNI · UniProt P76216