Crystal structure of ERAP2 aminopeptidase in complex with phosphinic pseudotripeptide ((1R)-1-amino-3-PHENYLPROPYL){2-([1,1:3,1- terphenyl]-5-ylmethyl)-3-[((2S)-1-amino-1-oxo-3-phenylpropan-2-yl)- amino]-3-OXOPROPYL}PHOSPHINIC acid

Structure

x-ray diffraction · 2 distinct chains · 44% helix, 20% strand (DSSP).

Ligands and binding sites

• 7OO · [(2~{S})-3-[[(2~{S})-1-azanyl-4-methyl-1-oxidanylidene-pentan-2-yl]amino]-2-[(3,5-diphenylphenyl)methyl]-3-oxidanylidene-propyl]-[(1~{R})-1-azanyl-3-phenyl-propyl]phosphinic acid · ligand · 2 copies · chains A, B
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 26 copies · chains A, B
• BMA · beta-D-mannopyranose · sugar · 4 copies · chains B, A
• MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A
• ZN · Zinc ion · metal · 2 copies · chains A, B
• EDO · 1,2-ethanediol · additive · 3 copies · chains A
• IMD · Imidazole · additive · chains A

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

Pockets

20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 584 Ų buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 17 glycan, 4 disulfide (N-glycosylation, disulfide).

Compared structures

• 7PFS · Crystal structure of ERAP2 aminopeptidase in complex with phosphinic pseudotripeptide… · the same entry in another collection · chain A against A, TM-score 1.00
• Q6P179 · AlphaFold monomer V2.0 prediction for endoplasmic reticulum aminopeptidase 2 (Q6P179) · 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 Q6P179
• Elsewhere: RCSB PDB 7PFS · PDBe 7PFS · UniProt Q6P179