High-resolution crystal structure of ERAP1 in complex with 10MER phosphinic peptide

Structure

x-ray diffraction · 2 distinct chains · 46% helix, 22% strand (DSSP).

Ligands and binding sites

• KF2 · [(1~{R})-1-azanyl-3-phenyl-propyl]-[(2~{S})-2-methanoyl-4-methyl-pentyl]phosphinic acid · ligand · chains A, B
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A
• FUC · alpha-L-fucopyranose · sugar
• BMA · beta-D-mannopyranose · sugar
• MAN · alpha-D-mannopyranose · sugar · chains A
• NA · Sodium ion · metal · 4 copies · chains A, B
• ZN · Zinc ion · metal · chains A
• SCN · Thiocyanate ion · ion · 11 copies · chains A, B
• EDO · 1,2-ethanediol · additive · 22 copies · chains A
• PGE · Triethylene glycol · additive · 3 copies · chains A

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

Pockets

7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 848 Ų buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 glycan, 1 covalent, 1 disulfide (N-glycosylation, covalent ligand, disulfide).

Compared structures

• 6RQX · High-resolution crystal structure of ERAP1 in complex with 10mer phosphinic peptide · 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 6RQX · PDBe 6RQX · UniProt Q9NZ08