SMTL ID : 8svm.1 (1 other biounit)

Plasmodium falciparum M17 aminopeptidase bound to MMV1557817

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-hexamer

Ligands

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

CO3.1: 7 residues within 4Å: Chain A: K.291, A.377, E.378, G.379, R.380, L.404 Ligands: WRC.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.291, A:G.379, A:R.380, A:L.404 CO3.10: 8 residues within 4Å: Chain B: K.291, A.377, E.378, G.379, R.380, L.404, T.405 Ligands: WRC.13 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.379, B:R.380, B:R.380, B:R.380 CO3.16: 9 residues within 4Å: Chain C: K.291, A.377, E.378, G.379, R.380, L.404, T.405 Ligands: ZN.17, WRC.19 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:A.377, C:G.379, C:R.380, C:L.404 CO3.25: 8 residues within 4Å: Chain D: K.291, A.377, E.378, G.379, R.380, L.404, T.405 Ligands: WRC.28 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.380, D:R.380, D:L.404 CO3.32: 10 residues within 4Å: Chain E: K.291, D.376, A.377, E.378, G.379, R.380, L.404, T.405 Ligands: ZN.33, WRC.35 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:R.380, E:R.380, E:L.404 CO3.39: 7 residues within 4Å: Chain F: A.377, E.378, G.379, R.380, L.404, T.405 Ligands: WRC.42 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:R.380, F:R.380, F:L.404

12 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: D.296, D.376, E.378 Ligands: ZN.3, WRC.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.296, A:D.376, A:D.376, A:E.378, WRC.4 ZN.3: 6 residues within 4Å: Chain A: K.291, D.296, D.316, E.378 Ligands: ZN.2, WRC.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.316, A:E.378 ZN.11: 6 residues within 4Å: Chain B: D.296, K.303, D.376, E.378 Ligands: ZN.12, WRC.13 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:D.296, B:D.376, B:D.376, B:E.378, WRC.13 ZN.12: 6 residues within 4Å: Chain B: K.291, D.296, D.316, E.378 Ligands: ZN.11, WRC.13 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.296, B:D.316, B:D.316, B:E.378 ZN.17: 7 residues within 4Å: Chain C: K.291, D.296, D.316, E.378 Ligands: CO3.16, ZN.18, WRC.19 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.296, C:D.316, C:E.378 ZN.18: 6 residues within 4Å: Chain C: D.296, K.303, D.376, E.378 Ligands: ZN.17, WRC.19 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.296, C:D.296, C:D.376, C:D.376, C:E.378 ZN.26: 6 residues within 4Å: Chain D: K.291, D.296, D.316, E.378 Ligands: ZN.27, WRC.28 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.296, D:D.316, D:E.378 ZN.27: 5 residues within 4Å: Chain D: D.296, D.376, E.378 Ligands: ZN.26, WRC.28 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Ligand interactions Metal complexes: D:D.296, D:D.376, D:D.376, D:E.378, WRC.28 ZN.33: 7 residues within 4Å: Chain E: K.291, D.296, D.316, E.378 Ligands: CO3.32, ZN.34, WRC.35 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.316, E:E.378 ZN.34: 6 residues within 4Å: Chain E: D.296, K.303, D.376, E.378 Ligands: ZN.33, WRC.35 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Ligand interactions Metal complexes: E:D.296, E:D.376, E:D.376, E:E.378, WRC.35 ZN.40: 6 residues within 4Å: Chain F: K.291, D.296, D.316, E.378 Ligands: ZN.41, WRC.42 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:D.316, F:D.316, F:E.378 ZN.41: 6 residues within 4Å: Chain F: D.296, K.303, D.376, E.378 Ligands: ZN.40, WRC.42 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Ligand interactions Metal complexes: F:D.296, F:D.376, F:D.376, F:E.378, WRC.42

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

WRC.4: 20 residues within 4Å: Chain A: K.291, D.296, K.303, G.307, M.309, F.315, D.316, D.376, A.377, E.378, L.404, T.405, G.406, L.409, S.471, A.494, F.500 Ligands: CO3.1, ZN.2, ZN.3 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.315, A:A.377 Hydrogen bonds: A:K.303, A:G.406 Water bridges: A:K.303 Halogen bonds: A:G.307 WRC.13: 21 residues within 4Å: Chain B: K.291, D.296, K.303, G.307, S.308, M.309, M.313, F.315, D.316, D.376, E.378, R.380, L.404, T.405, G.406, L.409, A.494, F.500 Ligands: CO3.10, ZN.11, ZN.12 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.315 Hydrogen bonds: B:K.303, B:G.406 Water bridges: B:K.303, B:D.376 Halogen bonds: B:G.307 WRC.19: 20 residues within 4Å: Chain C: K.291, D.296, K.303, G.307, M.309, F.315, D.316, N.374, D.376, A.377, E.378, L.404, T.405, G.406, L.409, A.494, F.500 Ligands: CO3.16, ZN.17, ZN.18 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:F.315, C:A.377 Hydrogen bonds: C:K.303, C:L.404, C:G.406 Water bridges: C:K.303, C:D.376, C:A.407 Halogen bonds: C:G.307 WRC.28: 20 residues within 4Å: Chain D: K.291, D.296, K.303, G.307, M.309, F.315, D.316, N.374, D.376, A.377, E.378, L.404, T.405, G.406, L.409, A.494, F.500 Ligands: CO3.25, ZN.26, ZN.27 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:F.315, D:A.377, D:A.494 Hydrogen bonds: D:K.291, D:K.303, D:L.404, D:G.406 Water bridges: D:K.303, D:D.376, D:S.471 WRC.35: 21 residues within 4Å: Chain E: K.291, D.296, K.303, G.307, M.309, F.315, D.316, D.376, A.377, E.378, R.380, L.404, T.405, G.406, L.409, S.471, A.494, F.500 Ligands: CO3.32, ZN.33, ZN.34 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:F.315, E:A.377 Hydrogen bonds: E:K.303, E:G.406 Halogen bonds: E:G.307 WRC.42: 20 residues within 4Å: Chain F: K.291, D.296, K.303, G.307, M.309, F.315, D.316, N.374, D.376, A.377, E.378, L.404, T.405, G.406, L.409, A.494, F.500 Ligands: CO3.39, ZN.40, ZN.41 7 PLIP interactions: 7 interactions with chain F Hydrophobic interactions: F:F.315, F:A.377, F:L.409 Hydrogen bonds: F:K.291, F:K.303, F:G.406 Water bridges: F:K.303

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

1PE.5: 7 residues within 4Å: Chain A: Y.20, N.21, H.25, F.206, K.237, Y.328 Ligands: 1PE.7 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Y.328, A:Y.328 1PE.6: 3 residues within 4Å: Chain A: G.36, N.39, Y.187 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.37 1PE.7: 6 residues within 4Å: Chain A: Y.20, E.233, Q.236, K.237 Ligands: 1PE.5, SO4.8 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.237 Hydrogen bonds: A:K.237 1PE.14: 6 residues within 4Å: Chain B: Y.20, H.25, F.206, K.237, Y.328 Ligands: 1PE.15 No protein-ligand interaction detected (PLIP) 1PE.15: 4 residues within 4Å: Chain B: Y.20, E.233, K.237 Ligands: 1PE.14 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:K.237 Hydrogen bonds: B:K.237 1PE.20: 6 residues within 4Å: Chain C: Y.20, N.21, E.233, K.237 Ligands: 1PE.21, SO4.23 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:K.237 Hydrogen bonds: C:K.237 1PE.21: 8 residues within 4Å: Chain C: Y.20, N.21, H.25, F.206, K.237, L.238, Y.328 Ligands: 1PE.20 No protein-ligand interaction detected (PLIP) 1PE.22: 4 residues within 4Å: Chain C: Y.32, G.37, N.39, Y.187 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.39, C:Y.187 1PE.29: 6 residues within 4Å: Chain D: Y.20, N.21, H.25, F.206, K.237, Y.328 No protein-ligand interaction detected (PLIP) 1PE.30: 4 residues within 4Å: Chain D: Y.20, N.21, E.233, K.237 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.21, D:K.237 Water bridges: D:E.233, D:E.233 1PE.36: 4 residues within 4Å: Chain E: Y.20, N.21, E.233, K.237 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:K.237 1PE.37: 6 residues within 4Å: Chain E: Y.20, N.21, H.25, F.206, K.237, Y.328 No protein-ligand interaction detected (PLIP) 1PE.38: 6 residues within 4Å: Chain E: S.10, L.11, D.12, P.13, T.14, Y.221 2 PLIP interactions: 2 interactions with chain E Water bridges: E:Q.7, E:T.14 1PE.43: 6 residues within 4Å: Chain F: Y.20, N.21, H.25, F.206, K.237, Y.328 2 PLIP interactions: 2 interactions with chain F Water bridges: F:N.21, F:T.332 1PE.44: 6 residues within 4Å: Chain D: S.171 Chain F: N.366, K.368, D.460, E.481, Q.484 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:D.460 Hydrogen bonds: F:K.368, F:E.481, F:Q.484

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

SO4.8: 5 residues within 4Å: Chain A: I.18, E.19, Y.20, N.21 Ligands: 1PE.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.20, A:N.21, A:N.21 SO4.9: 6 residues within 4Å: Chain A: S.352, K.353 Chain B: S.352, K.353 Chain C: S.352, K.353 8 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: C:S.352, C:K.353, A:K.353, B:S.352, B:K.353 Salt bridges: C:K.353, A:K.353, B:K.353 SO4.23: 5 residues within 4Å: Chain C: I.18, E.19, Y.20, N.21 Ligands: 1PE.20 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Y.20, C:N.21, C:N.21 Water bridges: C:N.21 SO4.24: 9 residues within 4Å: Chain C: F.73, N.78, M.79, K.81, F.82 Chain E: Y.93, M.94, F.95, S.101 3 PLIP interactions: 3 interactions with chain C Water bridges: C:N.78, C:K.81 Salt bridges: C:K.81 SO4.31: 7 residues within 4Å: Chain A: F.73, N.78, F.82 Chain D: Y.93, M.94, F.95, S.101 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.101, D:S.101 SO4.45: 6 residues within 4Å: Chain D: S.352, K.353 Chain E: S.352, K.353 Chain F: S.352, K.353 5 PLIP interactions: 1 interactions with chain F, 2 interactions with chain D, 2 interactions with chain E Hydrogen bonds: F:K.353, D:K.353, E:K.353 Salt bridges: D:K.353, E:K.353

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

Leucine aminopeptidase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Leucine aminopeptidase

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