SMTL ID : 7nup.1 (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

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-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.1: 7 residues within 4Å: Chain A: H.83, P.84, N.85, T.87, R.226, E.227, L.248 No protein-ligand interaction detected (PLIP)

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.2: 6 residues within 4Å: Chain A: N.219, T.255, T.256, V.257, K.258, Y.487 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.487 NAG-NAG.3: 5 residues within 4Å: Chain A: L.401, I.402, N.405, K.466, E.471 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 5 residues within 4Å: Chain A: H.370, H.374, E.393, Y.455 Ligands: USK.11 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.370, A:H.374, A:E.393

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

NAG.5: 1 residues within 4Å: Chain A: N.103 No protein-ligand interaction detected (PLIP) NAG.6: 3 residues within 4Å: Chain A: N.119, E.136, D.167 No protein-ligand interaction detected (PLIP) NAG.7: 2 residues within 4Å: Chain A: N.431, L.580 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 No protein-ligand interaction detected (PLIP) NAG.9: 1 residues within 4Å: Chain A: N.714 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.714 NAG.10: 4 residues within 4Å: Chain A: N.294, D.352, P.353, K.354 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.352

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: 18 residues within 4Å: Chain A: G.334, A.335, E.337, R.345, S.348, W.363, H.370, E.371, H.374, E.393, K.397, F.450, Y.455, Y.892, R.895 Ligands: ZN.4, BR.14, BR.20 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.450, A:Y.892, A:Y.892, A:Y.892 Hydrogen bonds: A:G.334, A:A.335, A:A.335, A:K.397, A:F.450, A:Y.455, A:R.895, A:R.895 pi-Stacking: A:W.363

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.12: 10 residues within 4Å: Chain A: K.354, T.355, W.777, G.782, L.784, N.785, I.786, L.791, Q.811, E.820 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.785, A:I.786, A:I.786, A:Q.811

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

EDO.13: 3 residues within 4Å: Chain A: Q.728, N.959, H.963 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.959

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

BR.14: 1 residues within 4Å: Ligands: USK.11 Ligand excluded by PLIP BR.15: 2 residues within 4Å: Chain A: E.311, Y.317 Ligand excluded by PLIP BR.16: 4 residues within 4Å: Chain A: F.905, S.906, S.907, K.910 Ligand excluded by PLIP BR.17: 2 residues within 4Å: Chain A: K.908, D.909 Ligand excluded by PLIP BR.18: 3 residues within 4Å: Chain A: R.345, E.346, T.347 Ligand excluded by PLIP BR.19: 1 residues within 4Å: Chain A: W.739 Ligand excluded by PLIP BR.20: 4 residues within 4Å: Chain A: A.332, G.334, R.345 Ligands: USK.11 Ligand excluded by PLIP BR.21: 3 residues within 4Å: Chain A: S.359, W.363, 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
A

Endoplasmic reticulum aminopeptidase 2

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