Structure of the periplasmic binding protein (pbp) noct from agrobacterium tumefaciens C58 in complex with octopinic acid

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 23% strand (DSSP).

Ligands and binding sites

• AQQ · (2~{S})-5-azanyl-2-[[(2~{R})-1-oxidanyl-1-oxidanylidene-propan-2-yl]amino]pentanoic acid · ligand · 2 copies · chains A, B
• EDO · 1,2-ethanediol · additive · 2 copies · chains A

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

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 654 Ų buried · 6 hydrogen bonds · protein-protein

Compared structures

• 5OTA · Structure of the periplasmic binding protein (PBP) NocT from Agrobacterium tumefaciens… · the same entry in another collection · chain A against A, TM-score 1.00
• P35120 · AlphaFold monomer V2.0 prediction for nopaline-binding periplasmic protein (P35120) · a predicted model of the same protein · 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 P35120
• Elsewhere: RCSB PDB 5OTA · PDBe 5OTA · UniProt P35120