SMTL ID : 4jbs.2 (1 other biounit)

Crystal structure of the human Endoplasmic Reticulum Aminopeptidase 2 in complex with PHOSPHINIC PSEUDOTRIPEPTIDE inhibitor.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.79 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- MAN- MAN: alpha-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN-MAN.1: 6 residues within 4Å: Chain A: H.83, P.84, N.85, E.227, G.246, L.248 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.246

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 6 residues within 4Å: Chain A: H.77, N.219, T.255, V.257, K.258, Y.487 No protein-ligand interaction detected (PLIP)

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.3: 1 residues within 4Å: Chain A: N.431 No protein-ligand interaction detected (PLIP) NAG.4: 1 residues within 4Å: Chain A: N.294 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.294

1 x ZN: ZINC ION(Non-covalent)

ZN.5: 4 residues within 4Å: Chain A: H.370, H.374, E.393 Ligands: P52.6 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.370, A:H.374, A:E.393, A:E.393

1 x P52: Nalpha-[(2S)-2-{[[(1R)-1-amino-3-phenylpropyl](hydroxy)phosphoryl]methyl}-4-methylpentanoyl]-L-tryptophanamide(Non-covalent)

P52.6: 15 residues within 4Å: Chain A: E.200, G.334, A.335, M.336, E.337, V.367, H.370, E.371, K.392, E.393, F.450, E.452, Y.455, Y.892 Ligands: ZN.5 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.367, A:E.452, A:Y.892, A:Y.892 Hydrogen bonds: A:E.200, A:G.334, A:E.393, A:Y.455, A:Y.455 pi-Stacking: A:F.450

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zervoudi, E. et al., Rationally designed inhibitor targeting antigen-trimming aminopeptidases enhances antigen presentation and cytotoxic T-cell responses. Proc.Natl.Acad.Sci.USA (2013)

Release Date

2013-12-11

Peptides

Endoplasmic reticulum aminopeptidase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Endoplasmic reticulum aminopeptidase 2

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