SMTL ID : 5lhd.2 (3 other biounits)

Structure of glycosylated human aminopeptidase N

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

monomer

Ligands

1 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)

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)

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: K.224, S.238, P.240, N.248 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: K.275, Y.299, N.302 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain A: D.416, Q.579, L.607, N.608, V.638 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.413 NAG-NAG.7: 3 residues within 4Å: Chain A: N.664, L.667, E.947 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.947

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.5: 1 residues within 4Å: Chain A: N.510 No protein-ligand interaction detected (PLIP)

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

NAG.8: 2 residues within 4Å: Chain A: N.767, N.801 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.801 Hydrogen bonds: A:N.767

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.4

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

EDO.10: 2 residues within 4Å: Chain A: P.223, W.247 No protein-ligand interaction detected (PLIP) EDO.11: 2 residues within 4Å: Chain A: D.271, Y.272 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.271 EDO.12: 8 residues within 4Å: Chain A: F.378, G.379, V.382, I.384, L.392, N.393, Y.486, T.495 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.393, A:Y.486, A:Y.486 Water bridges: A:I.384 EDO.13: 6 residues within 4Å: Chain A: T.71, R.73, K.87, G.88, S.89, I.221 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.89 EDO.14: 6 residues within 4Å: Chain A: L.114, G.117, H.118, R.119, K.135, T.136 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.119, A:R.119, A:T.136 EDO.15: 7 residues within 4Å: Chain A: R.58, E.209, P.210, A.211, M.212, E.385, W.386 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.209, A:A.211, A:E.385 EDO.16: 3 residues within 4Å: Chain A: P.306, Y.407, A.408 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.408 EDO.17: 4 residues within 4Å: Chain A: R.525, F.563, V.566, I.586 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.525, A:R.525, A:F.563, A:I.586 EDO.18: 7 residues within 4Å: Chain A: L.604, V.615, Y.617, W.622, Q.643, I.644, D.647 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.605, A:V.615, A:V.615, A:Y.617, A:D.647 EDO.19: 5 residues within 4Å: Chain A: F.352, P.354, S.357, S.358, S.359 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.354, A:S.359 EDO.20: 7 residues within 4Å: Chain A: H.296, L.351, D.353, S.357, L.804, V.805, N.806 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.357, A:V.805, A:N.806, A:N.806 EDO.21: 5 residues within 4Å: Chain A: A.99, S.152, L.153, V.154, K.155 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.152, A:K.155 Water bridges: A:A.99

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
B

Aminopeptidase N

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