SMTL ID : 5lds.1 (2 other biounits)

Structure of the porcine aminopeptidase N ectodomain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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.1: 2 residues within 4Å: Chain A: N.628, V.631 No protein-ligand interaction detected (PLIP)

6 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: 7 residues within 4Å: Chain A: S.62, Y.63, N.64, R.88, N.211, T.248 Ligands: NAG.11 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.88, A:R.88 NAG-NAG.3: 4 residues within 4Å: Chain A: V.180, K.182, N.219, E.263 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.182, A:K.182 NAG-NAG.4: 4 residues within 4Å: Chain A: D.410, M.574, N.604, I.635 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 7 residues within 4Å: Chain B: S.62, Y.63, N.64, R.88, N.211, T.248 Ligands: NAG.17 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.88, B:R.88 NAG-NAG.6: 4 residues within 4Å: Chain B: V.180, K.182, N.219, E.263 1 PLIP interactions: 1 interactions with chain B Water bridges: B:K.182 NAG-NAG.7: 5 residues within 4Å: Chain B: D.410, M.574, V.603, N.604, I.635 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.8: 5 residues within 4Å: Chain A: H.365, H.369, E.388, Y.454 Ligands: ACT.12 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.365, A:H.369, A:E.388, ACT.12 ZN.13: 5 residues within 4Å: Chain B: H.365, H.369, E.388, Y.454 Ligands: ACT.18 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:H.365, B:H.369, B:E.388, ACT.18

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

NAG.9: 5 residues within 4Å: Chain A: L.78, N.106, Q.160, G.161, E.162 No protein-ligand interaction detected (PLIP) NAG.10: 4 residues within 4Å: Chain A: A.205, F.484, Q.487, N.488 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.488 Water bridges: A:Q.487, A:N.488 NAG.11: 5 residues within 4Å: Chain A: N.64, I.86, E.154, E.245 Ligands: NAG-NAG.2 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.86 Hydrogen bonds: A:E.245 Water bridges: A:N.64 NAG.14: 5 residues within 4Å: Chain B: L.78, N.106, Q.160, G.161, E.162 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.106 NAG.15: 4 residues within 4Å: Chain B: A.205, F.484, Q.487, N.488 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.488 Water bridges: B:N.488, B:N.488 NAG.16: 3 residues within 4Å: Chain B: N.628, S.630, V.631 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.628, B:N.628 NAG.17: 5 residues within 4Å: Chain B: N.64, I.86, E.154, E.245 Ligands: NAG-NAG.5 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.86 Hydrogen bonds: B:E.245 Water bridges: B:N.64, B:N.64

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.12: 8 residues within 4Å: Chain A: A.330, E.332, H.365, E.366, H.369, E.388, Y.454 Ligands: ZN.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.330 Salt bridges: A:H.365, A:H.369 ACT.18: 8 residues within 4Å: Chain B: A.330, E.332, H.365, E.366, H.369, E.388, Y.454 Ligands: ZN.13 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.454 Salt bridges: B:H.365, B:H.369

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Aminopeptidase N

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