SMTL ID : 7rie.1 (1 other biounit)

Plasmodium falciparum M17 in complex with inhibitor MIPS2571

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.49 Å

Oligo State

homo-hexamer

Ligands

6 x CO3: CARBONATE ION(Non-functional Binders)

CO3.1: 8 residues within 4Å: Chain A: K.290, A.376, E.377, G.378, R.379, L.403, T.404 Ligands: 5IF.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.379, A:R.379, A:L.403 CO3.6: 8 residues within 4Å: Chain B: K.290, A.376, E.377, G.378, R.379, L.403, T.404 Ligands: 5IF.11 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.376, B:G.378, B:R.379, B:L.403 CO3.12: 8 residues within 4Å: Chain C: K.290, A.376, E.377, G.378, R.379, L.403, T.404 Ligands: 5IF.18 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.378, C:R.379, C:R.379, C:R.379 CO3.19: 7 residues within 4Å: Chain D: K.290, A.376, E.377, G.378, R.379, L.403 Ligands: 5IF.22 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.378, D:R.379, D:L.403 CO3.23: 7 residues within 4Å: Chain E: K.290, A.376, E.377, G.378, R.379, L.403 Ligands: 5IF.29 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:G.378, E:R.379, E:R.379, E:R.379 CO3.30: 8 residues within 4Å: Chain F: K.290, A.376, E.377, G.378, R.379, L.403, T.404 Ligands: 5IF.34 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:G.378, F:R.379, F:R.379, F:R.379

12 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain A: K.290, D.295, D.315, E.377 Ligands: ZN.3, 5IF.5 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.295, A:D.315, A:E.377, H2O.1 ZN.3: 5 residues within 4Å: Chain A: D.295, D.375, E.377 Ligands: ZN.2, 5IF.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.295, A:D.375, A:D.375, A:E.377 ZN.7: 6 residues within 4Å: Chain B: K.290, D.295, D.315, E.377 Ligands: ZN.8, 5IF.11 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.295, B:D.315, B:E.377, H2O.7 ZN.8: 6 residues within 4Å: Chain B: D.295, K.302, D.375, E.377 Ligands: ZN.7, 5IF.11 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.295, B:D.295, B:D.375, B:D.375, B:E.377 ZN.13: 6 residues within 4Å: Chain C: K.290, D.295, D.315, E.377 Ligands: ZN.14, 5IF.18 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.295, C:D.315, C:E.377, H2O.11 ZN.14: 6 residues within 4Å: Chain C: D.295, K.302, D.375, E.377 Ligands: ZN.13, 5IF.18 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.295, C:D.375, C:D.375, C:E.377 ZN.20: 6 residues within 4Å: Chain D: K.290, D.295, D.315, E.377 Ligands: ZN.21, 5IF.22 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.295, D:D.315, D:D.315, D:E.377, H2O.14 ZN.21: 6 residues within 4Å: Chain D: D.295, K.302, D.375, E.377 Ligands: ZN.20, 5IF.22 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.295, D:D.375, D:D.375, D:E.377 ZN.24: 6 residues within 4Å: Chain E: K.290, D.295, D.315, E.377 Ligands: ZN.25, 5IF.29 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.295, E:D.315, E:E.377, H2O.22 ZN.25: 5 residues within 4Å: Chain E: D.295, D.375, E.377 Ligands: ZN.24, 5IF.29 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.295, E:D.295, E:D.375, E:D.375, E:E.377 ZN.31: 6 residues within 4Å: Chain F: K.290, D.295, D.315, E.377 Ligands: ZN.32, 5IF.34 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.295, F:D.315, F:E.377, H2O.26 ZN.32: 6 residues within 4Å: Chain F: D.295, K.302, D.375, E.377 Ligands: ZN.31, 5IF.34 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:D.295, F:D.295, F:D.375, F:D.375, F:E.377

5 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.4: 6 residues within 4Å: Chain A: Y.19, N.20, H.24, F.205, K.236, Y.327 No protein-ligand interaction detected (PLIP) 1PE.10: 4 residues within 4Å: Chain B: Y.19, H.24, K.236, Y.327 No protein-ligand interaction detected (PLIP) 1PE.16: 6 residues within 4Å: Chain C: Y.19, N.20, H.24, F.205, K.236, Y.327 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.20 1PE.17: 5 residues within 4Å: Chain C: S.9, L.10, D.11, P.12, T.13 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.13 1PE.28: 5 residues within 4Å: Chain E: Y.19, H.24, F.205, K.236, Y.327 1 PLIP interactions: 1 interactions with chain E Water bridges: E:Y.327

6 x 5IF: N-{(1R)-2-(hydroxyamino)-1-[4'-(hydroxymethyl)[1,1'-biphenyl]-4-yl]-2-oxoethyl}-2,2-dimethylpropanamide(Non-covalent)

5IF.5: 19 residues within 4Å: Chain A: K.290, D.295, K.302, M.308, L.311, M.312, D.375, E.377, G.378, L.403, T.404, G.405, L.408, S.470, A.493, F.499 Ligands: CO3.1, ZN.2, ZN.3 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.408 Hydrogen bonds: A:K.302, A:D.375, A:E.377, A:G.378, A:G.405 Water bridges: A:S.470 pi-Cation interactions: A:K.302 5IF.11: 17 residues within 4Å: Chain B: K.290, D.295, K.302, L.311, M.312, D.375, E.377, G.378, L.403, T.404, G.405, L.408, A.493, F.499 Ligands: CO3.6, ZN.7, ZN.8 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.311, B:L.408 Hydrogen bonds: B:K.290, B:K.302, B:D.375, B:E.377, B:G.378, B:G.405 Water bridges: B:S.470 5IF.18: 18 residues within 4Å: Chain C: K.290, D.295, K.302, M.308, L.311, M.312, D.375, E.377, L.403, T.404, G.405, L.408, S.470, A.493, F.499 Ligands: CO3.12, ZN.13, ZN.14 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:L.311, C:L.408 Hydrogen bonds: C:K.290, C:K.302, C:D.375, C:E.377, C:L.403, C:G.405 Water bridges: C:D.295, C:D.295, C:S.470 5IF.22: 18 residues within 4Å: Chain D: K.290, D.295, K.302, S.307, M.308, L.311, D.375, E.377, G.378, L.403, T.404, G.405, L.408, A.493, F.499 Ligands: CO3.19, ZN.20, ZN.21 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:L.311, D:L.408 Hydrogen bonds: D:K.290, D:K.302, D:D.375, D:E.377, D:G.378, D:G.405 5IF.29: 16 residues within 4Å: Chain E: K.290, D.295, K.302, M.308, D.375, E.377, T.402, L.403, T.404, G.405, L.408, A.493, F.499 Ligands: CO3.23, ZN.24, ZN.25 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:L.408 Hydrogen bonds: E:K.290, E:K.302, E:D.375, E:L.403, E:G.405 Water bridges: E:A.406 5IF.34: 14 residues within 4Å: Chain F: K.290, D.295, K.302, D.375, E.377, L.403, T.404, G.405, L.408, A.493, F.499 Ligands: CO3.30, ZN.31, ZN.32 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:L.408 Hydrogen bonds: F:K.302, F:D.375, F:L.403, F:G.405

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

SO4.9: 6 residues within 4Å: Chain A: S.351, K.352 Chain B: S.351, K.352 Chain C: S.351, K.352 7 PLIP interactions: 2 interactions with chain C, 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: C:K.352, A:S.351, A:K.352, B:K.352 Salt bridges: C:K.352, A:K.352, B:K.352 SO4.15: 1 residues within 4Å: Chain C: E.423 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.423, C:E.423 SO4.26: 6 residues within 4Å: Chain D: S.351, K.352 Chain E: S.351, K.352 Chain F: S.351, K.352 8 PLIP interactions: 3 interactions with chain E, 2 interactions with chain D, 3 interactions with chain F Hydrogen bonds: E:S.351, E:K.352, D:K.352, F:S.351, F:K.352 Salt bridges: E:K.352, D:K.352, F:K.352 SO4.27: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.427 SO4.33: 5 residues within 4Å: Chain F: S.2, E.3, V.4, T.13, N.228 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:S.2, F:V.4, F:N.228 Water bridges: F:T.13

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Edgar, R.C.S. et al., Genetic and chemical validation of Plasmodium falciparum aminopeptidase Pf A-M17 as a drug target in the hemoglobin digestion pathway. Elife (2022)

Release Date

2022-09-14

Peptides

M17 leucyl aminopeptidase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

M17 leucyl aminopeptidase

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