SMTL ID : 5j6s.2 (1 other biounit)

Crystal structure of Endoplasmic Reticulum Aminopeptidase 2 (ERAP2) in complex with a hydroxamic derivative ligand

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.1: 7 residues within 4Å: Chain A: H.83, P.84, N.85, R.226, E.227, G.246, L.248 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.246

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

NAG-NAG-BMA.2: 6 residues within 4Å: Chain A: N.219, T.255, T.256, V.257, K.258, Y.487 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: H.370, H.374, E.393 Ligands: 6GA.9 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.370, A:H.374, A:E.393, A:E.393

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

NAG.4: 1 residues within 4Å: Chain A: N.103 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.103 NAG.5: 1 residues within 4Å: Chain A: N.294 No protein-ligand interaction detected (PLIP) NAG.6: 3 residues within 4Å: Chain A: N.405, D.414, K.466 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.405, A:D.414, A:K.466 NAG.7: 4 residues within 4Å: Chain A: N.431, K.545, E.576, E.936 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.431, A:K.545 NAG.8: 1 residues within 4Å: Chain A: N.650 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.650

1 x 6GA: (2S)-N~1~-benzyl-2-[(4-fluorophenyl)methyl]-N~3~-hydroxypropanediamide(Non-covalent)

6GA.9: 14 residues within 4Å: Chain A: D.198, E.200, P.333, A.335, M.336, E.337, H.370, E.371, H.374, E.393, F.450, Y.455, Y.892 Ligands: ZN.3 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.333, A:P.333, A:F.450 Hydrogen bonds: A:A.335, A:Y.455 pi-Stacking: A:Y.892

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mpakali, A. et al., Crystal Structures of ERAP2 Complexed with Inhibitors Reveal Pharmacophore Requirements for Optimizing Inhibitor Potency. ACS Med Chem Lett (2017)

Release Date

2017-03-15

Peptides

Endoplasmic reticulum aminopeptidase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Endoplasmic reticulum aminopeptidase 2

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