SMTL ID : 8slo.1

Plasmodium falciparum M1 aminopeptidase bound to selective inhibitor MIPS2673

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 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: BYW.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.496, A:H.500, A:E.519, A:E.519

1 x BYW: 2-hydroxy-N-[(1R)-2-(hydroxyamino)-2-oxo-1-(3',4',5'-trifluoro[1,1'-biphenyl]-4-yl)ethyl]-2-methylpropanamide(Non-covalent)

BYW.2: 21 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, H.496, E.497, H.500, E.519, M.571, E.572, Y.575, Y.580, M.1034 Ligands: ZN.1, GOL.9 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:V.459, A:V.459, A:Y.575, A:Y.580 Hydrogen bonds: A:G.460, A:A.461, A:A.461, A:R.489, A:R.489, A:Y.580, A:Y.580 pi-Stacking: A:Y.575 Halogen bonds: A:M.571

5 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 1 residues within 4Å: Chain A: E.957 No protein-ligand interaction detected (PLIP) MG.4: 1 residues within 4Å: Chain A: E.526 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.526, H2O.8, H2O.10, H2O.31, H2O.40 MG.5: 1 residues within 4Å: Chain A: G.250 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:G.250, H2O.14, H2O.20, H2O.27, H2O.31 MG.6: 1 residues within 4Å: Chain A: D.438 No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Chain A: N.1083 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 6 residues within 4Å: Chain A: A.303, T.305, R.325, E.572, P.1033, N.1073 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.305, A:T.305, A:E.572 Water bridges: A:R.325 GOL.9: 6 residues within 4Å: Chain A: Y.575, T.576, T.577, Y.580, D.581 Ligands: BYW.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.577, A:D.581

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Giannangelo, C. et al., Chemoproteomics validates selective targeting of Plasmodium M1 alanyl aminopeptidase as a cross-species strategy to treat malaria. Elife (2024)

Release Date

2024-04-03

Peptides

M1 family aminopeptidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

M1 family aminopeptidase

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