SMTL ID : 4jbs.1 (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

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

NAG-NAG.1: 6 residues within 4Å: Chain A: H.83, N.85, R.226, E.227, G.246, L.248 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.246 NAG-NAG.2: 5 residues within 4Å: Chain A: N.219, T.256, V.257, K.258, Y.487 No protein-ligand interaction detected (PLIP)

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

NAG.3: 2 residues within 4Å: Chain A: N.405, D.414 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.405 NAG.4: 3 residues within 4Å: Chain A: N.650, T.652, L.653 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.650 NAG.5: 1 residues within 4Å: Chain A: N.103 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.6: 5 residues within 4Å: Chain A: H.370, H.374, E.393, Y.455 Ligands: P52.7 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.370, A:H.374, A:E.393

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

P52.7: 16 residues within 4Å: Chain A: E.200, G.334, A.335, M.336, E.337, V.367, H.370, E.371, H.374, K.392, E.393, F.450, D.451, Y.455, Y.892 Ligands: ZN.6 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:E.200, A:V.367, A:Y.892, A:Y.892 Hydrogen bonds: A:G.334, A:K.392, A:E.393, A:F.450 pi-Stacking: A:F.450

2 x IMD: IMIDAZOLE(Non-covalent)

IMD.8: 3 residues within 4Å: Chain A: H.708, K.756, R.865 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.712 pi-Stacking: A:H.708 IMD.9: 7 residues within 4Å: Chain A: L.122, S.124, Y.130, V.152, E.154, L.156, Y.162 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.154, A:E.154 pi-Stacking: A:Y.130

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
A

Endoplasmic reticulum aminopeptidase 2

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