Crystal structure of the porcine carboxypeptidase B - anabaenopeptin F complex

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 17% strand (DSSP).

Ligands and binding sites

• 73N · (2~{S})-5-carbamimidamido-2-(carboxyamino)pentanoic acid · ligand · 3 copies · chains A, F, B, G, C, H
• 73O · (2~{S})-2-azanyl-4-(4-hydroxyphenyl)butanoic acid · ligand · 3 copies · chains A, F, B, G, C, H
• ZN · Zinc ion · metal · 3 copies · chains A, F, B, G, C

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

Pockets

6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Interfaces

6 interfaces between chains.

• A–C · 535 Ų buried · 2 hydrogen bonds · protein-protein
• C–H · 288 Ų buried · 4 hydrogen bonds · protein-protein
• A–F · 281 Ų buried · 5 hydrogen bonds · protein-protein
• B–G · 280 Ų buried · 4 hydrogen bonds · protein-protein
• B–C · 206 Ų buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 covalent, 9 disulfide, 6 modified, 3 d-amino, 3 isopeptide (covalent ligand, disulfide, nonstandard, D-amino acid, isopeptide).

Compared structures

• 5LRK · Crystal structure of the porcine carboxypeptidase B - Anabaenopeptin F complex · the same entry in another collection · chain H against H, TM-score 1.00
• P09955 · AlphaFold monomer V2.0 prediction for carboxypeptidase B (P09955) · 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 P09955
• Elsewhere: RCSB PDB 5LRK · PDBe 5LRK · UniProt P09955