High-resolution crystal structure of ERAP1 with bound phosphinic transition-state analogue inhibitor

Structure

x-ray diffraction · 1 distinct chain · 46% helix, 22% strand (DSSP).

Ligands and binding sites

• HJ5 · [(1~{R})-1-[[(2~{S})-2-[[(2~{S})-1-azaniumyl-1-oxidanylidene-3-phenyl-propan-2-yl]carbamoyl]pent-4-ynyl]-oxidanyl-phosphoryl]-3-phenyl-propyl]azanium · ligand · chains A
• MLT · D-malate · ligand · chains A
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A
• BMA · beta-D-mannopyranose · sugar · chains A
• NA · Sodium ion · metal · 3 copies · chains A
• ZN · Zinc ion · metal · chains A
• EDO · 1,2-ethanediol · additive · 30 copies · chains A
• B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · chains A
• P6G · Hexaethylene glycol · additive · chains A
• PG4 · Tetraethylene glycol · additive · chains A

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

Pockets

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

Modifications

Observed in the structure: 4 glycan, 2 disulfide (N-glycosylation, disulfide).

Compared structures

• 6Q4R · High-resolution crystal structure of ERAP1 with bound phosphinic transition-state… · the same entry in another collection · chain A against A, TM-score 1.00
• Q9NZ08 · AlphaFold monomer V2.0 prediction for endoplasmic reticulum aminopeptidase 1 (Q9NZ08) · 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 Q9NZ08
• Elsewhere: RCSB PDB 6Q4R · PDBe 6Q4R · UniProt Q9NZ08