SMTL ID : 7srv.1

Metal dependent activation of Plasmodium falciparum M17 aminopeptidase (inactive form), spacegroup P22121

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.03 Å

Oligo State

homo-hexamer

Ligands

12 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: D.295, D.310, D.375, E.377 Chain C: K.302 Ligands: ZN.6 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.310, A:D.375, A:E.377, H2O.4, H2O.9 ZN.6: 5 residues within 4Å: Chain A: D.295, D.310, M.312, D.315 Ligands: ZN.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.310, A:D.310, A:M.312, A:D.315, H2O.4 ZN.7: 6 residues within 4Å: Chain A: K.302 Chain B: D.295, D.310, D.375, E.377 Ligands: ZN.13 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.295, B:D.310, B:D.375, B:E.377, H2O.18 ZN.13: 6 residues within 4Å: Chain A: K.302 Chain B: D.295, D.310, M.312, D.315 Ligands: ZN.7 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.310, B:M.312, B:D.315, H2O.2, H2O.18 ZN.14: 6 residues within 4Å: Chain B: K.302 Chain C: D.295, D.310, D.375, E.377 Ligands: ZN.25 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.310, C:D.375, C:E.377, H2O.27, H2O.32 ZN.25: 5 residues within 4Å: Chain C: D.295, D.310, M.312, D.315 Ligands: ZN.14 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.310, C:M.312, H2O.17, H2O.27, H2O.31 ZN.26: 6 residues within 4Å: Chain D: D.295, D.310, D.375, E.377 Chain F: K.302 Ligands: ZN.32 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.310, D:D.375, D:E.377, H2O.38, H2O.43 ZN.32: 5 residues within 4Å: Chain D: D.295, D.310, M.312, D.315 Ligands: ZN.26 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.310, D:M.312, D:D.315, H2O.38, H2O.67 ZN.33: 6 residues within 4Å: Chain D: K.302 Chain E: D.295, D.310, D.375, E.377 Ligands: ZN.40 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.310, E:D.375, E:D.375, E:E.377, H2O.51 ZN.40: 5 residues within 4Å: Chain E: D.295, D.310, M.312, D.315 Ligands: ZN.33 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.310, E:M.312, E:D.315, H2O.51, H2O.56 ZN.41: 6 residues within 4Å: Chain E: K.302 Chain F: D.295, D.310, D.375, E.377 Ligands: ZN.47 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.310, F:D.375, F:E.377, H2O.65, H2O.67 ZN.47: 5 residues within 4Å: Chain F: D.295, D.310, M.312, D.315 Ligands: ZN.41 5 PLIP interactions: 2 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:D.310, F:M.312, H2O.65, H2O.66, H2O.70

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

CO3.2: 6 residues within 4Å: Chain A: D.375, A.376, E.377, G.378, R.379, L.403 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.377, A:G.378, A:R.379, A:R.379, A:R.379 CO3.8: 6 residues within 4Å: Chain B: D.375, 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 CO3.15: 6 residues within 4Å: Chain C: D.375, A.376, E.377, G.378, R.379, L.403 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.377, C:G.378, C:R.379, C:R.379, C:R.379 CO3.27: 5 residues within 4Å: Chain D: A.376, E.377, G.378, R.379, L.403 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.375, D:R.379, D:R.379 Water bridges: D:G.378 CO3.34: 6 residues within 4Å: Chain E: D.375, A.376, E.377, G.378, R.379, L.403 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:D.375, E:R.379, E:R.379 Water bridges: E:G.378 CO3.42: 6 residues within 4Å: Chain F: D.375, A.376, E.377, G.378, R.379, L.403 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:D.375, F:R.379, F:R.379 Water bridges: F:G.378

8 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 7 residues within 4Å: Chain A: M.308, R.379, I.463, S.464, V.467, S.470, V.473 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.464, A:S.470 Salt bridges: A:R.379 ACT.9: 6 residues within 4Å: Chain B: R.379, I.463, S.464, V.467, S.470, V.473 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.464, B:S.464 Salt bridges: B:R.379 ACT.16: 6 residues within 4Å: Chain C: R.379, I.463, S.464, V.467, S.470, V.473 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.464 Salt bridges: C:R.379 ACT.24: 4 residues within 4Å: Chain C: W.441, W.442 Chain D: W.441, W.442 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:W.441 Water bridges: D:W.441 ACT.28: 6 residues within 4Å: Chain D: R.379, I.463, S.464, V.467, S.470, V.473 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.464, D:S.464 Salt bridges: D:R.379 ACT.31: 2 residues within 4Å: Chain D: N.421, N.422 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.422 ACT.35: 7 residues within 4Å: Chain E: M.308, R.379, I.463, S.464, V.467, S.470, V.473 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:S.464, E:S.470 Salt bridges: E:R.379 ACT.46: 6 residues within 4Å: Chain F: R.379, I.463, S.464, V.467, S.470, V.473 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:S.464, F:S.464 Salt bridges: F:R.379

12 x CA: CALCIUM ION(Non-covalent)

CA.4: 8 residues within 4Å: Chain A: K.290, F.314, D.315, M.316, S.317, G.318, A.401, T.402 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.402 CA.11: 8 residues within 4Å: Chain B: K.290, F.314, D.315, M.316, S.317, G.318, A.401, T.402 No protein-ligand interaction detected (PLIP) CA.12: 2 residues within 4Å: Chain B: E.18, N.20 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:N.20 CA.17: 8 residues within 4Å: Chain C: K.290, F.314, D.315, M.316, S.317, G.318, A.401, T.402 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.402 CA.18: 1 residues within 4Å: Chain C: E.480 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.480, H2O.34 CA.19: 2 residues within 4Å: Chain C: H.522 Ligands: EDO.23 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.522, H2O.29 CA.20: 2 residues within 4Å: Chain C: N.49, E.143 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.143, H2O.33 CA.29: 8 residues within 4Å: Chain D: K.290, F.314, D.315, M.316, S.317, G.318, A.401, T.402 No protein-ligand interaction detected (PLIP) CA.36: 8 residues within 4Å: Chain E: K.290, F.314, D.315, M.316, S.317, G.318, A.401, T.402 No protein-ligand interaction detected (PLIP) CA.37: 2 residues within 4Å: Chain E: E.40, N.97 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.40, E:E.40, H2O.49, H2O.51 CA.38: 1 residues within 4Å: Chain E: E.195 3 PLIP interactions: 2 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.195, E:E.195, H2O.55 CA.44: 8 residues within 4Å: Chain F: K.290, F.314, D.315, M.316, S.317, G.318, A.401, T.402 No protein-ligand interaction detected (PLIP)

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 2 residues within 4Å: Chain A: N.422, A.486 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.422 EDO.21: 2 residues within 4Å: Chain C: R.167, Y.220 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.220 EDO.22: 2 residues within 4Å: Chain C: I.214, A.215 No protein-ligand interaction detected (PLIP) EDO.23: 4 residues within 4Å: Chain C: H.522, H.523, H.524 Ligands: CA.19 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.524 EDO.30: 7 residues within 4Å: Chain D: K.428, Q.431, S.432, E.514, F.515, N.518, D.519 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.518, D:D.519 Water bridges: D:Q.431 EDO.45: 2 residues within 4Å: Chain F: N.421, N.422 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.422

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.10: 6 residues within 4Å: Chain A: S.351, K.352 Chain B: S.351, K.352 Chain C: S.351, K.352 11 PLIP interactions: 3 interactions with chain B, 4 interactions with chain C, 4 interactions with chain A Hydrogen bonds: B:K.352, C:S.351, C:S.351, C:K.352, A:S.351, A:K.352 Water bridges: B:N.353, A:K.352 Salt bridges: B:K.352, C:K.352, A:K.352 PO4.43: 6 residues within 4Å: Chain D: S.351, K.352 Chain E: S.351, K.352 Chain F: S.351, K.352 7 PLIP interactions: 2 interactions with chain E, 4 interactions with chain F, 1 interactions with chain D Hydrogen bonds: E:K.352, F:S.351, F:K.352, D:K.352 Salt bridges: E:K.352, F:K.352 Water bridges: F:K.352

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.39: 6 residues within 4Å: Chain D: G.358, E.370 Chain E: A.215, A.216, P.217, K.313 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:G.358, E:K.313, E:K.313

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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