SMTL ID : 7nsk.1 (1 other biounit)

Endoplasmic reticulum aminopeptidase 2 complexed with a hydroxamic ligand

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 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: 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

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: 1 residues within 4Å: Chain A: N.103 No protein-ligand interaction detected (PLIP)

3 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.3: 7 residues within 4Å: Chain A: N.219, T.255, T.256, V.257, K.258, Y.487 Ligands: P4G.11 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.487 NAG-NAG-BMA.4: 3 residues within 4Å: Chain A: N.405, D.414, K.466 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 3 residues within 4Å: Chain A: N.650, T.652, L.653 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.6: 5 residues within 4Å: Chain A: H.370, E.371, H.374, E.393 Ligands: UQE.12 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.370, A:H.374, A:E.393

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

NAG.7: 2 residues within 4Å: Chain A: T.118, N.119 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.118, A:N.119 NAG.8: 1 residues within 4Å: Chain A: N.714 No protein-ligand interaction detected (PLIP) NAG.9: 1 residues within 4Å: Chain A: N.294 No protein-ligand interaction detected (PLIP) NAG.10: 2 residues within 4Å: Chain A: N.431, K.545 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.545

1 x P4G: 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE(Non-covalent)

P4G.11: 2 residues within 4Å: Chain A: S.486 Ligands: NAG-NAG-BMA.3 No protein-ligand interaction detected (PLIP)

1 x UQE: (2~{S})-3-(4-hydroxyphenyl)-~{N}-oxidanyl-2-[4-[[(5-pyridin-2-ylthiophen-2-yl)sulfonylamino]methyl]-1,2,3-triazol-1-yl]propanamide(Non-covalent)

UQE.12: 15 residues within 4Å: Chain A: E.200, P.333, G.334, A.335, E.337, H.370, E.371, H.374, E.393, E.400, Q.447, F.450, Y.455, Y.892 Ligands: ZN.6 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.333 Hydrogen bonds: A:E.200, A:E.400, A:Y.892 pi-Stacking: A:H.370, A:Y.892

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

EDO.13: 2 residues within 4Å: Chain A: L.100, H.159 No protein-ligand interaction detected (PLIP) EDO.14: 2 residues within 4Å: Chain A: A.857, H.860 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.860 EDO.15: 7 residues within 4Å: Chain A: W.777, L.784, N.785, I.786, L.791, Y.795, E.820 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.786, A:I.786, A:Y.795 EDO.16: 4 residues within 4Å: Chain A: K.305, A.406, T.407, E.410 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.410 EDO.17: 1 residues within 4Å: Chain A: D.79 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mpakali, A. et al., Endoplasmic reticulum aminopeptidase 2 in complex with a phosphinic 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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