SMTL ID : 5lhd.1 (3 other biounits)

Structure of glycosylated human aminopeptidase N

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

monomer

Ligands

2 x NAG- NAG- BMA- BMA: beta-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-BMA.1: 6 residues within 4Å: Chain A: L.83, V.85, N.111, E.166, G.167, E.168 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-BMA.6: 6 residues within 4Å: Chain A: Q.626, T.660, N.664, L.667, Q.943, W.944 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.943, A:Q.943

1 x NAG- NAG- BMA- BMA- BMA: beta-D-mannopyranose-(1-3)-[beta-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-BMA-BMA.2: 6 residues within 4Å: Chain A: S.67, Y.68, R.69, R.93, N.217, T.254 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.3: 6 residues within 4Å: Chain A: H.222, K.224, L.226, S.238, P.240, N.248 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain A: D.416, Q.579, N.608, V.638, I.639 No protein-ligand interaction detected (PLIP)

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.4: 2 residues within 4Å: Chain A: Y.299, N.302 No protein-ligand interaction detected (PLIP)

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

NAG.7: 1 residues within 4Å: Chain A: N.510 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.510 NAG.8: 2 residues within 4Å: Chain A: E.797, N.801 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.797 Hydrogen bonds: A:E.797, A:E.797, A:N.801

1 x ZN: ZINC ION(Non-covalent)

ZN.9: 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.2

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

EDO.10: 4 residues within 4Å: Chain A: S.741, S.745, T.778, N.782 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain A: D.66, T.95, K.97, Q.158 Ligand excluded by PLIP EDO.12: 7 residues within 4Å: Chain A: P.354, S.357, S.359, K.362, H.772, N.774 Ligands: EDO.25 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain A: S.115, V.121, D.162, S.163, E.164 Ligands: EDO.19 Ligand excluded by PLIP EDO.14: 7 residues within 4Å: Chain A: R.58, E.209, P.210, A.211, M.212, E.385, W.386 Ligand excluded by PLIP EDO.15: 7 residues within 4Å: Chain A: P.60, T.62, L.63, T.100, V.102, I.103, I.104 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain A: T.71, K.87, G.88, S.89, I.221 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain A: A.99, S.152, L.153, V.154, K.155 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain A: S.107, K.108, K.109, L.138 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain A: S.89, S.90, T.91, D.162, S.163 Ligands: EDO.13 Ligand excluded by PLIP EDO.20: 6 residues within 4Å: Chain A: Q.196, A.197, A.198, D.199, P.448, S.452 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain A: G.236, P.237, T.239, V.249, E.251 Ligand excluded by PLIP EDO.22: 4 residues within 4Å: Chain A: Y.319, P.320, L.321, P.322 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain A: V.429, S.434, S.435, D.456, I.458 Ligand excluded by PLIP EDO.24: 3 residues within 4Å: Chain A: D.502, H.503, E.506 Ligand excluded by PLIP EDO.25: 5 residues within 4Å: Chain A: K.362, W.412, E.728, Q.733 Ligands: EDO.12 Ligand excluded by PLIP EDO.26: 8 residues within 4Å: Chain A: Y.68, S.90, T.91, V.92, M.161, D.162, S.163, P.205 Ligand excluded by PLIP

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
A

Aminopeptidase N

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