SMTL ID : 5y3i.1

Crystal structure of Plasmodium falciparum aminopeptidase N in complex with (S)-N-hydroxy-4-methyl-2-(3-(3-methylbenzyl)ureido)pentanamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.325, H.329, E.348 Ligands: 8N3.5, GOL.6 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.325, A:H.329, A:E.348, A:E.348

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 1 residues within 4Å: Chain A: G.79 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:G.79, H2O.5, H2O.19, H2O.20 MG.3: 1 residues within 4Å: Chain A: E.786 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain A: E.355 Ligands: GOL.6 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:E.355, H2O.2, H2O.10, H2O.17, H2O.18, H2O.23

1 x 8N3: (2R)-4-methyl-2-[(3-methylphenyl)methylcarbamoylamino]-N-oxidanyl-pentanamide(Non-covalent)

8N3.5: 18 residues within 4Å: Chain A: Q.146, E.148, V.288, G.289, A.290, M.291, E.292, H.325, E.326, H.329, E.348, Y.404, T.405, T.406, Y.409, D.410 Ligands: ZN.1, GOL.6 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:E.148, A:V.288, A:Y.404, A:Y.404, A:Y.409 Hydrogen bonds: A:G.289, A:A.290, A:A.290, A:Y.409 Water bridges: A:R.318 pi-Stacking: A:Y.409

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 8 residues within 4Å: Chain A: R.318, V.322, H.325, E.326, Y.409 Ligands: ZN.1, MG.4, 8N3.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.318, A:R.318, A:H.325, A:E.326 Water bridges: A:G.289 GOL.7: 9 residues within 4Å: Chain A: N.287, V.288, G.289, N.300, N.302, S.303, R.318, N.823, R.826 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.300, A:N.302, A:N.302, A:S.303, A:R.318, A:R.318, A:R.826 Water bridges: A:G.289 GOL.8: 5 residues within 4Å: Chain A: Y.682, S.732, L.733, K.736, Y.767 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.732 GOL.9: 8 residues within 4Å: Chain A: M.362, T.363, K.364, H.715, V.716, D.717, F.718, D.719 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:M.362, A:D.717, A:F.718, A:D.719 Water bridges: A:V.716, A:V.716

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Marapaka, A.K. et al., Crystal structure of Plasmodium falciparum aminopeptidase N in complex with (S)-N-hydroxy-4-methyl-2-(3-(3-methylbenzyl)ureido)pentanamide. To Be Published

Release Date

2018-08-08

Peptides

M1 family aminopeptidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

M1 family aminopeptidase

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