Crystal structure of the N-terminal beta-aminopeptidase bapa in complex with hydrolyzed ampicillin

Structure

x-ray diffraction · 4 distinct chains · 29% helix, 28% strand (DSSP).

Ligands and binding sites

• OAE · (2S,4S)-2-[(R)-{[(2R)-2-amino-2-phenylacetyl]amino}(carboxy)methyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid · ligand · 6 copies · chains A, C, B, D
• SO4 · Sulfate ion · ion · 4 copies · chains A, D, B, C
• GOL · Glycerol · additive · 4 copies · chains A, B, C, D

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

Pockets

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

Interfaces

6 interfaces between chains.

• B–D · 1781 Ų buried · 16 hydrogen bonds · protein-protein
• A–C · 1777 Ų buried · 18 hydrogen bonds · protein-protein
• A–D · 1515 Ų buried · 23 hydrogen bonds · protein-protein
• B–C · 1465 Ų buried · 23 hydrogen bonds · protein-protein
• A–B · 917 Ų buried · 12 hydrogen bonds · protein-protein

Compared structures

• 3NFB · Crystal structure of the N-terminal beta-aminopeptidase BapA in complex with hydrolyzed… · the same entry in another collection · chain D against D, TM-score 1.00
• Q52VH2 · AlphaFold monomer V2.0 prediction for beta-peptidyl aminopeptidase bapa (Q52VH2) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 Q52VH2
• Elsewhere: RCSB PDB 3NFB · PDBe 3NFB · UniProt Q52VH2