SMTL ID : 8svl.1

Plasmodium falciparum M1 aminopeptidase bound to MMV1557817

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.496, H.500, E.519 Ligands: WRC.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.496, A:H.500, A:E.519, A:E.519, WRC.2

1 x WRC: N-[(1R)-2-(hydroxyamino)-2-oxo-1-(3',4',5'-trifluoro[1,1'-biphenyl]-4-yl)ethyl]-3,3-dimethylbutanamide

WRC.2: 22 residues within 4Å: Chain A: T.305, Q.317, E.319, A.320, N.458, V.459, G.460, A.461, E.463, R.489, V.493, H.496, E.497, H.500, E.519, M.571, E.572, Y.575, Y.580, M.1034 Ligands: ZN.1, GOL.6 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.459, A:V.459, A:V.493, A:Y.575, A:Y.580 Hydrogen bonds: A:G.460, A:A.461, A:Y.580, A:Y.580 pi-Stacking: A:Y.575 Halogen bonds: A:N.458, A:M.571

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: A.303, T.305, R.325, E.572, P.1033, N.1073 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.305, A:T.305, A:E.572 GOL.4: 5 residues within 4Å: Chain A: H.653, Y.741, E.743, N.835, F.836 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.676, A:Y.741, A:N.835 Water bridges: A:E.743 GOL.5: 6 residues within 4Å: Chain A: N.573, Y.575, T.576, T.1037, Q.1038, Y.1077 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:N.573, A:Y.575, A:T.1037, A:T.1037 Water bridges: A:Y.575, A:Q.1038, A:Y.1077, A:Y.1077, A:Y.1077, A:Y.1077 GOL.6: 5 residues within 4Å: Chain A: Y.575, T.576, T.577, Y.580 Ligands: WRC.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.576 Water bridges: A:G.460, A:T.577 GOL.7: 5 residues within 4Å: Chain A: S.826, Y.853, T.900, S.903, L.904 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.853, A:Y.853, A:T.900, A:S.903 GOL.8: 8 residues within 4Å: Chain A: V.459, G.460, N.471, N.473, S.474, R.489, N.994, R.997 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.471, A:N.473, A:N.473, A:S.474, A:S.474, A:R.489, A:R.997 Water bridges: A:G.460, A:Q.1038 GOL.9: 9 residues within 4Å: Chain A: D.545, Y.765, C.768, T.769, Y.772, Y.823, S.826, L.827, P.828 6 PLIP interactions: 6 interactions with chain A Water bridges: A:D.545, A:D.545, A:R.548, A:Q.829, A:Q.829, A:Q.829 GOL.10: 3 residues within 4Å: Chain A: H.886, V.887, D.888 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.887, A:V.887 Water bridges: A:V.887, A:F.889, A:F.889

5 x MG: MAGNESIUM ION(Non-covalent)

MG.11: 1 residues within 4Å: Chain A: G.250 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:G.250, H2O.18, H2O.19, H2O.30, H2O.32, H2O.34 MG.12: 1 residues within 4Å: Chain A: D.438 No protein-ligand interaction detected (PLIP) MG.13: 2 residues within 4Å: Chain A: Q.666, S.668 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.668, H2O.5, H2O.13, H2O.29 MG.14: 1 residues within 4Å: Chain A: E.957 No protein-ligand interaction detected (PLIP) MG.15: 2 residues within 4Å: Chain A: T.492, E.526 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

de Koning-Ward, T.F. et al., Characterisation of a novel antimalarial agent targeting haemaglobin digestion that shows cross-species reactivity and excellent in vivo properties. Mbio (2024)

Release Date

2024-04-24

Peptides

M1 family aminopeptidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

M1 family aminopeptidase

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