SMTL ID : 5lhd.4 (3 other biounits)

Structure of glycosylated human aminopeptidase N

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

monomer

Ligands

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.1: 6 residues within 4Å: Chain A: L.83, V.85, N.111, E.166, G.167, E.168 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.168 NAG-NAG-BMA.3: 5 residues within 4Å: Chain A: K.224, L.226, S.238, P.240, N.248 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 3 residues within 4Å: Chain A: K.275, Y.299, N.302 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- BMA- BMA- BMA: beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-6)-[beta-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-BMA-BMA-BMA.2: 7 residues within 4Å: Chain A: S.67, Y.68, R.69, R.93, N.217, K.235, T.254 No protein-ligand interaction detected (PLIP)

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.5: 2 residues within 4Å: Chain A: N.556, T.558 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 7 residues within 4Å: Chain A: N.413, D.416, Q.579, L.607, N.608, V.638, I.639 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain A: Q.626, N.664, L.667 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain A: N.718, N.719 No protein-ligand interaction detected (PLIP)

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

NAG.9: 1 residues within 4Å: Chain A: N.510 No protein-ligand interaction detected (PLIP) NAG.10: 2 residues within 4Å: Chain A: E.797, N.801 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.11: 3 residues within 4Å: Chain A: H.371, H.375, E.394 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.371, A:H.375, A:E.394, H2O.3

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

EDO.12: 8 residues within 4Å: Chain A: F.352, S.357, S.358, S.359, K.362, I.726, H.772, N.774 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.362, A:N.774, A:N.774 EDO.13: 4 residues within 4Å: Chain A: S.398, E.401, D.422, Y.460 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.422 EDO.14: 8 residues within 4Å: Chain A: F.473, P.570, I.571, T.572, D.582, Y.583, W.584 Ligands: EDO.15 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.584 Water bridges: A:S.472, A:S.472 EDO.15: 5 residues within 4Å: Chain A: S.472, T.572, Q.579, D.582 Ligands: EDO.14 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.472, A:Q.579 EDO.16: 5 residues within 4Å: Chain A: L.551, N.650, S.653, Y.687, K.926 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.926, A:K.926

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Santiago, C. et al., Allosteric inhibition of aminopeptidase N functions related to tumor growth and virus infection. Sci Rep (2017)

Release Date

2017-04-05

Peptides

Aminopeptidase N: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

Aminopeptidase N

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