SMTL ID : 7t3v.1

Metal dependent activation of Plasmodium falciparum M17 aminopeptidase, spacegroup P22121 after crystals soaked with Zn2+

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: 6 residues within 4Å: Chain A: A.376, E.377, G.378, R.379, L.403, T.404 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.376, A:G.378, A:R.379, A:R.379, A:R.379 CO3.4: 5 residues within 4Å: Chain B: A.376, E.377, G.378, R.379, L.403 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.376, B:G.378, B:R.379, B:L.403 CO3.8: 7 residues within 4Å: Chain C: K.290, D.375, A.376, E.377, G.378, R.379, L.403 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.375, C:G.378, C:R.379 CO3.13: 6 residues within 4Å: Chain D: D.375, A.376, E.377, G.378, R.379, L.403 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:E.377, D:G.378, D:R.379, D:R.379 CO3.16: 6 residues within 4Å: Chain E: K.290, A.376, E.377, G.378, R.379, L.403 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:R.379, E:R.379, E:L.403 CO3.20: 6 residues within 4Å: Chain F: D.375, A.376, E.377, G.378, R.379, L.403 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:A.376, F:E.377, F:G.378

12 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: D.295, D.315, D.375, E.377 Ligands: ZN.3 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.295, A:D.375, A:D.375, A:E.377, A:E.377 ZN.3: 5 residues within 4Å: Chain A: K.290, D.295, D.315, E.377 Ligands: ZN.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.295, A:D.315, A:E.377 ZN.5: 5 residues within 4Å: Chain B: K.290, D.295, D.315, E.377 Ligands: ZN.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.295, B:D.315, B:E.377 ZN.6: 4 residues within 4Å: Chain B: D.295, D.375, E.377 Ligands: ZN.5 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.295, B:D.375, B:D.375, B:E.377 ZN.9: 5 residues within 4Å: Chain C: K.290, D.295, D.315, E.377 Ligands: ZN.10 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.315, C:E.377 ZN.10: 4 residues within 4Å: Chain C: D.295, D.375, E.377 Ligands: ZN.9 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.375, C:D.375, C:E.377, C:E.377 ZN.14: 5 residues within 4Å: Chain D: K.290, D.295, D.315, E.377 Ligands: ZN.15 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.295, D:D.315, D:E.377, H2O.8 ZN.15: 6 residues within 4Å: Chain D: D.295, K.302, D.315, D.375, E.377 Ligands: ZN.14 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.295, D:D.375, D:D.375, D:E.377, H2O.8 ZN.17: 5 residues within 4Å: Chain E: K.290, D.295, D.315, E.377 Ligands: ZN.18 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:D.295, E:D.315, E:E.377 ZN.18: 4 residues within 4Å: Chain E: D.295, D.375, E.377 Ligands: ZN.17 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.295, E:D.375, E:D.375, E:E.377 ZN.21: 6 residues within 4Å: Chain F: D.295, K.302, D.315, D.375, E.377 Ligands: ZN.22 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.295, F:D.375, F:D.375, F:E.377, H2O.11 ZN.22: 6 residues within 4Å: Chain F: K.290, D.295, D.315, D.375, E.377 Ligands: ZN.21 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.295, F:D.315, F:E.377, H2O.11

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.7: 10 residues within 4Å: Chain A: V.7, V.8 Chain C: V.246, L.258, G.261, K.262, S.264, Y.266, P.267, N.268 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:V.7, A:V.8 Hydrogen bonds: C:N.268, C:N.268 MPD.12: 9 residues within 4Å: Chain D: V.246, L.258, G.261, K.262, Y.266, P.267, N.268 Chain E: V.7, V.8 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: D:P.267, D:N.268, E:V.8 Hydrogen bonds: D:G.261, D:K.262

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

SO4.11: 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: 3 interactions with chain A, 3 interactions with chain C, 1 interactions with chain B Hydrogen bonds: A:S.351, A:K.352, C:S.351, C:K.352, B:K.352 Salt bridges: A:K.352, C:K.352 SO4.19: 6 residues within 4Å: Chain D: S.351, K.352 Chain E: S.351, K.352 Chain F: S.351, K.352 6 PLIP interactions: 3 interactions with chain E, 2 interactions with chain F, 1 interactions with chain D Hydrogen bonds: E:K.352, F:K.352, D:K.352 Water bridges: E:S.351 Salt bridges: E:K.352, F:K.352

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Webb, C.T. et al., A metal ion-dependent conformational switch modulates activity of the Plasmodium M17 aminopeptidase. J.Biol.Chem. (2022)

Release Date

2022-06-29

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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