SMTL ID : 5yo1.1

Structure of ePepN E298A mutant in complex with Puromycin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.318, H.322, E.341, Y.402 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.318, A:H.322, A:E.341, A:E.341, H2O.25

2 x PUY: PUROMYCIN(Non-covalent)

PUY.2: 15 residues within 4Å: Chain A: M.281, R.314, V.315, H.318, D.348, Y.397, L.399, Y.402, E.403, R.804, G.808, R.846, L.847 Ligands: PUY.3, GOL.12 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:R.804, A:R.846, A:L.847 Hydrogen bonds: A:R.846 Water bridges: A:A.283, A:K.295, A:K.295 pi-Stacking: A:H.318, A:Y.402 PUY.3: 9 residues within 4Å: Chain A: Y.296, D.311, R.314, V.315, T.368, L.372, L.399, E.403 Ligands: PUY.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.296, A:V.315 Hydrogen bonds: A:T.368, A:E.403 Water bridges: A:N.365, A:T.368

1 x NA: SODIUM ION(Non-functional Binders)

NA.4: 6 residues within 4Å: Chain A: Y.39, R.65, S.69, A.71, N.106, L.107 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.39, A:R.65, A:S.69, A:N.106, A:L.107 Water bridges: A:N.106

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: A.552, L.553, W.567, S.584, D.587, A.588, S.591 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.553, A:D.587, A:S.591, A:S.591 Water bridges: A:F.557 GOL.6: 4 residues within 4Å: Chain A: L.82, V.83, W.95 Ligands: GOL.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.83 GOL.7: 7 residues within 4Å: Chain A: S.84, V.85, W.92, T.93, W.95 Ligands: GOL.6, GOL.14 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.85, A:V.85, A:W.95 GOL.8: 6 residues within 4Å: Chain A: R.662, E.663, T.666, R.707, F.711, A.743 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.662, A:R.707 Water bridges: A:A.659, A:R.662, A:T.666, A:R.707, A:A.743 GOL.9: 8 residues within 4Å: Chain A: M.576, R.577, R.585, A.619, A.622, V.623, D.626, I.629 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.585, A:D.626 GOL.10: 5 residues within 4Å: Chain A: E.144, D.333, W.334, F.335, V.390 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.144, A:W.334 Water bridges: A:K.29, A:E.144, A:V.390, A:M.393 GOL.11: 2 residues within 4Å: Chain A: H.32, R.35 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.35 Water bridges: A:H.32, A:D.33, A:R.35 GOL.12: 9 residues within 4Å: Chain A: E.376, N.395, Y.397, T.398, L.399, R.846, E.849, K.885 Ligands: PUY.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.376, A:L.399, A:K.885, A:K.885 Water bridges: A:E.376, A:Y.397, A:Y.397 GOL.13: 6 residues within 4Å: Chain A: D.302, F.725, M.731, A.734, K.759, W.760 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.759, A:W.760 Water bridges: A:D.302, A:K.759 GOL.14: 3 residues within 4Å: Chain A: T.93, W.95 Ligands: GOL.7 No protein-ligand interaction detected (PLIP) GOL.15: 4 residues within 4Å: Chain A: A.122, Q.132, G.134, F.278 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.122, A:Q.132, A:G.134 Water bridges: A:N.124 GOL.16: 4 residues within 4Å: Chain A: R.74, E.98, A.101, V.103 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.98 Water bridges: A:R.74, A:N.76

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Reddi, R. et al., Puromycin, a selective inhibitor of PSA acts as a substrate for other M1 family aminopeptidases: Biochemical and structural basis. Int.J.Biol.Macromol. (2020)

Release Date

2018-11-07

Peptides

Aminopeptidase N: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Aminopeptidase N