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

Structure

x-ray diffraction · 3 distinct chains · 28% helix, 29% strand (DSSP).

Ligands and binding sites

• AIC · (2S,5R,6R)-6-{[(2R)-2-amino-2-phenylethanoyl]amino}-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid · ligand · 4 copies · chains A, B, C, D
• NDV · (2S,4S)-2-[(1R)-1-{[(2R)-2-amino-2-phenylacetyl]amino}-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid · ligand · 2 copies · chains A, D
• GOL · Glycerol · additive · 4 copies · chains A, C, B, D

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

Pockets

8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Interfaces

6 interfaces between chains.

• C–D · 1793 Ų buried · 17 hydrogen bonds · protein-protein
• A–B · 1786 Ų buried · 17 hydrogen bonds · protein-protein
• B–C · 1452 Ų buried · 25 hydrogen bonds · protein-protein
• A–D · 1439 Ų buried · 24 hydrogen bonds · protein-protein
• B–D · 923 Ų buried · 14 hydrogen bonds · protein-protein

Compared structures

• 3NDV · Crystal structure of the N-terminal beta-aminopeptidase BapA in complex with ampicillin · 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 3NDV · PDBe 3NDV · UniProt Q52VH2