SMTL ID : 7nup.2 (3 other biounits)

Endoplasmic reticulum aminopeptidase 2 complexed with a mixed hydroxamic and sulfonyl ligand

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

monomer

Ligands

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

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

NAG-NAG.3: 4 residues within 4Å: Chain A: N.405, D.414, K.466, E.471 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain A: N.431, K.545, L.580, E.582, Y.584 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.582 NAG-NAG.5: 2 residues within 4Å: Chain A: N.650, T.652 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain A: N.714, S.716 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.7: 4 residues within 4Å: Chain A: H.370, H.374, E.393 Ligands: USK.11 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.370, A:H.374, A:E.393, A:E.393

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

NAG.8: 1 residues within 4Å: Chain A: N.103 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.103 NAG.9: 1 residues within 4Å: Chain A: N.294 No protein-ligand interaction detected (PLIP) NAG.10: 3 residues within 4Å: Chain A: N.119, T.121, E.136 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.121, A:E.136

1 x USK: (3~{S})-4-(4-hydroxyphenyl)-~{N}-oxidanyl-3-[5-[[(5-phenylthiophen-2-yl)sulfonylamino]methyl]-1,2,3-triazol-1-yl]butanamide(Non-covalent)

USK.11: 17 residues within 4Å: Chain A: A.332, G.334, A.335, E.337, R.345, R.366, H.370, E.371, H.374, E.393, K.397, F.450, Y.455, Y.892, R.895 Ligands: ZN.7, BR.13 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.450, A:Y.892, A:Y.892 Hydrogen bonds: A:G.334, A:A.335, A:R.366, A:K.397, A:F.450, A:Y.455, A:R.895, A:R.895 pi-Stacking: A:W.363, A:H.370

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.12: 2 residues within 4Å: Chain A: D.174, K.885 No protein-ligand interaction detected (PLIP)

2 x BR: BROMIDE ION(Non-functional Binders)(Non-covalent)

BR.13: 1 residues within 4Å: Ligands: USK.11 Ligand excluded by PLIP BR.14: 2 residues within 4Å: Chain A: L.362, R.366 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mpakali, A. et al., Endoplasmic reticulum aminopeptidase 2 complexed with a mixed hydroxamic and sulfonyl ligand. To Be Published

Release Date

2022-06-22

Peptides

Endoplasmic reticulum aminopeptidase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Endoplasmic reticulum aminopeptidase 2

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