SMTL ID : 6bv0.1

Crystal structure of porcine aminopeptidase-N with Arginine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

monomer

Ligands

3 x NAG- NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-NAG.1: 7 residues within 4Å: Chain A: N.20, I.42, E.110, K.185 Ligands: NAG-NAG.3, SO4.14, SO4.21 No protein-ligand interaction detected (PLIP) NAG-NAG-NAG.2: 5 residues within 4Å: Chain A: I.36, N.62, Q.116, G.117, E.118 No protein-ligand interaction detected (PLIP) NAG-NAG-NAG.5: 3 residues within 4Å: Chain A: Y.249, N.252, K.312 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.3: 9 residues within 4Å: Chain A: S.18, Y.19, N.20, R.44, N.167, T.204 Ligands: NAG-NAG-NAG.1, NAG-NAG-NAG.1, SO4.21 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.44, A:R.44 NAG-NAG.4: 3 residues within 4Å: Chain A: K.138, N.175, E.219 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.138 NAG-NAG.6: 1 residues within 4Å: Chain A: N.266 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 5 residues within 4Å: Chain A: L.15, A.161, F.440, Q.443, N.444 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.443 NAG-NAG.8: 4 residues within 4Å: Chain A: D.489, T.492, N.494, Q.541 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain A: N.363, D.366, V.559, N.560 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.363

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

NAG.10: 2 residues within 4Å: Chain A: E.505, N.507 No protein-ligand interaction detected (PLIP) NAG.11: 3 residues within 4Å: Chain A: N.584, S.586, V.587 No protein-ligand interaction detected (PLIP)

1 x ARG: ARGININE(Non-covalent)

ARG.12: 11 residues within 4Å: Chain A: Q.144, Q.146, A.284, A.286, M.287, E.288, E.322, E.344, F.405, Y.410 Ligands: ZN.23 10 PLIP interactions: 7 interactions with chain A, 3 Ligand-Ligand interactions Hydrogen bonds: A:A.286, A:E.344, A:E.344, A:Y.410, R.12 Water bridges: A:Q.144, A:Q.146, R.12, R.12 Salt bridges: A:H.321

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

SO4.13: 7 residues within 4Å: Chain A: P.160, Y.211, T.333, L.334, W.336, W.337, L.340 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.334 Water bridges: A:Y.211, A:Y.211 SO4.14: 7 residues within 4Å: Chain A: N.20, V.21, T.22, N.167, I.168, T.169 Ligands: NAG-NAG-NAG.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.21, A:T.169 Water bridges: A:N.20, A:T.22, A:F.202 SO4.15: 6 residues within 4Å: Chain A: G.285, A.286, R.296, A.299, R.314, V.318 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.285 Salt bridges: A:R.314 SO4.16: 6 residues within 4Å: Chain A: T.22, R.24, K.38, G.39, K.40, I.171 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.24, A:K.38 Water bridges: A:G.39 SO4.17: 2 residues within 4Å: Chain A: K.654, R.658 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.654, A:R.658 SO4.18: 5 residues within 4Å: Chain A: Y.349, L.353, K.365, R.418, N.422 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.349, A:N.422 Water bridges: A:R.418, A:R.418 Salt bridges: A:K.365, A:R.418 SO4.19: 4 residues within 4Å: Chain A: R.24, L.191, E.193, D.194 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.193, A:E.193 Water bridges: A:R.24, A:R.24, A:R.24, A:Y.26 Salt bridges: A:R.24 SO4.20: 4 residues within 4Å: Chain A: F.405, D.406, S.407, Y.410 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.405 SO4.21: 8 residues within 4Å: Chain A: N.167, K.185, E.201, F.202, T.204 Ligands: NAG-NAG-NAG.1, NAG-NAG-NAG.1, NAG-NAG.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.201, A:T.204 Water bridges: A:T.204 Salt bridges: A:K.185 SO4.22: 2 residues within 4Å: Chain A: Q.1, R.7 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.1 Water bridges: A:R.7, A:R.7, A:R.7, A:R.7 Salt bridges: A:R.7

1 x ZN: ZINC ION(Non-covalent)

ZN.23: 4 residues within 4Å: Chain A: H.321, H.325, E.344 Ligands: ARG.12 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.321, A:H.325, A:E.344, A:E.344, H2O.11

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joshi, S. et al., The Rational Design of Therapeutic Peptides for Aminopeptidase N using a Substrate-Based Approach. Sci Rep (2017)

Release Date

2018-01-17

Peptides

Aminopeptidase N: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Aminopeptidase N

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