Crystal structure of activated porcine pancreatic carboxypeptidase B [((R)-benzyloxycarbonylamino-cyclohexyl- methyl)-hydroxy-phosphinoyloxy]-(3-guanidino-phenyl)- acetic acid complex

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 16% strand (DSSP).

Ligands and binding sites

• 414 · (5R,6R,8S)-8-(3-{[amino(imino)methyl]amino}phenyl)-5-cyclohexyl-6-hydroxy-3-oxo-1-phenyl-2,7-dioxa-4-aza-6-phosphanonan-9-oic acid 6-oxide · ligand · 2 copies · chains A, B
• ZN · Zinc ion · metal · 2 copies · chains A, B

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

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 466 Ų buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

• 2PJ4 · CRYSTAL STRUCTURE OF ACTIVATED PORCINE PANCREATIC CARBOXYPEPTIDASE B… · the same entry in another collection · chain A against A, TM-score 1.00
• P09955 · AlphaFold monomer V2.0 prediction for carboxypeptidase B (P09955) · a predicted model of the same protein · chain B 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 2PJ4 · PDBe 2PJ4 · UniProt P09955