SMTL ID : 4nz8.1

Crystal structure of porcine aminopeptidase-N complexed with cleaved poly-alanine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

2 x ALA: CLEAVED poly-Ala(Non-covalent)

ALA.1: 8 residues within 4Å: Chain A: Q.145, A.285, M.286, E.287, E.343, Y.409 Ligands: ALA-ALA-ALA-ALA-ALA-ALA.2, ZN.13 Protein-ligand interaction information (PLIP) not available ALA.2: 15 residues within 4Å: Chain A: G.284, A.285, A.298, R.313, T.316, V.317, H.320, E.321, E.350, Y.351, P.369, G.370, D.371, R.374 Ligands: ALA.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:A.285, A:A.298, A:V.317, A:V.317, A:P.369 Hydrogen bonds: A:R.313, A:R.313, A:E.321 Water bridges: A:R.295, A:H.320, A:Y.351, A:S.634

5 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: N.19, I.41, E.109, K.184, E.200 Ligands: NAG-NAG.4 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 7 residues within 4Å: Chain A: S.17, Y.18, N.19, R.43, N.166, T.203 Ligands: NAG-NAG.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.43 Water bridges: A:R.43, A:R.43 NAG-NAG.5: 4 residues within 4Å: Chain A: T.27, K.137, N.174, E.218 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.137 NAG-NAG.6: 5 residues within 4Å: Chain A: L.14, A.160, F.439, Q.442, N.443 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.442 NAG-NAG.7: 5 residues within 4Å: Chain A: N.362, D.365, M.529, V.558, N.559 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.362

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

NAG.8: 5 residues within 4Å: Chain A: I.35, N.61, Q.115, G.116, E.117 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.35 Hydrogen bonds: A:N.61, A:Q.115 NAG.9: 5 residues within 4Å: Chain A: Y.248, N.251, F.301, P.303, K.311 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.248, A:F.301, A:P.303 Hydrogen bonds: A:N.251, A:K.311 NAG.10: 1 residues within 4Å: Chain A: N.265 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.265 Water bridges: A:N.265 NAG.11: 2 residues within 4Å: Chain A: D.488, N.493 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.493 NAG.12: 3 residues within 4Å: Chain A: N.583, S.585, V.586 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.583

1 x ZN: ZINC ION(Non-covalent)

ZN.13: 4 residues within 4Å: Chain A: H.320, H.324, E.343 Ligands: ALA.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.320, A:H.324, A:E.343, A:E.343, H2O.24

10 x SO4: SULFATE ION(Non-functional Binders)

SO4.14: 4 residues within 4Å: Chain A: Y.348, K.364, R.417, N.421 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Y.348, A:N.421 Water bridges: A:K.364, A:K.364, A:R.417, A:R.417 Salt bridges: A:K.364, A:R.417 SO4.15: 2 residues within 4Å: Chain A: G.739, Q.740 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.740 Water bridges: A:G.739, A:G.739 SO4.16: 7 residues within 4Å: Chain A: L.278, P.279, D.280, R.295, E.296, N.297, V.756 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.280, A:D.280, A:D.280, A:E.296, A:N.297 Water bridges: A:E.296 Salt bridges: A:R.295 SO4.17: 6 residues within 4Å: Chain A: T.21, R.23, K.37, G.38, K.39, I.170 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.38 Water bridges: A:R.23, A:G.38, A:F.114 SO4.18: 3 residues within 4Å: Chain A: P.255, N.258, H.356 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.255, A:N.258 Salt bridges: A:H.356 SO4.19: 5 residues within 4Å: Chain A: F.404, D.405, S.406, Y.409 Ligands: SO4.21 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.404 SO4.20: 4 residues within 4Å: Chain A: Q.630, Y.685, I.688, N.689 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.689 SO4.21: 3 residues within 4Å: Chain A: D.405, S.406 Ligands: SO4.19 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.406 Water bridges: A:I.407 SO4.22: 8 residues within 4Å: Chain A: P.159, Y.210, T.332, L.333, W.335, W.336, L.339, N.342 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.210, A:N.342 Water bridges: A:L.333, A:L.333 SO4.23: 5 residues within 4Å: Chain A: M.131, E.132, G.133, R.237, N.239 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.133, A:R.237, A:N.239 Water bridges: A:M.131, A:E.132

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, L. et al., Structural basis for multifunctional roles of mammalian aminopeptidase N. Proc.Natl.Acad.Sci.USA (2012)

Release Date

2013-12-25

Peptides

Aminopeptidase N: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Aminopeptidase N