SMTL ID : 6ee2.1 (1 other biounit)

X-ray crystal structure of Pf-M17 in complex with inhibitor 6i and regulatory zinc ion

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 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: J1V.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.379, A:R.379, A:L.403 CO3.13: 7 residues within 4Å: Chain B: K.290, A.376, E.377, G.378, R.379, L.403 Ligands: J1V.15 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.376, B:G.378, B:R.379, B:L.403 CO3.20: 7 residues within 4Å: Chain C: K.290, A.376, E.377, G.378, R.379, L.403 Ligands: J1V.22 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.379, C:R.379, C:L.403 CO3.27: 7 residues within 4Å: Chain D: K.290, A.376, E.377, G.378, R.379, L.403 Ligands: J1V.29 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:A.376, D:G.378, D:R.379, D:L.403 CO3.37: 8 residues within 4Å: Chain E: K.290, A.376, E.377, G.378, R.379, L.403, T.404 Ligands: J1V.39 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:G.378, E:R.379, E:R.379, E:R.379 CO3.46: 8 residues within 4Å: Chain F: K.290, A.376, E.377, G.378, R.379, L.403, T.404 Ligands: J1V.48 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:G.378, F:R.379, F:R.379, F:R.379

6 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: D.295, K.302, D.375, E.377 Ligands: J1V.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.295, A:D.375, A:D.375, A:E.377, J1V.3 ZN.14: 5 residues within 4Å: Chain B: D.295, K.302, D.375, E.377 Ligands: J1V.15 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:D.295, B:D.375, B:D.375, B:E.377, J1V.15 ZN.21: 5 residues within 4Å: Chain C: D.295, K.302, D.375, E.377 Ligands: J1V.22 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:D.295, C:D.375, C:D.375, C:E.377, J1V.22 ZN.28: 5 residues within 4Å: Chain D: D.295, K.302, D.375, E.377 Ligands: J1V.29 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Ligand interactions Metal complexes: D:D.295, D:D.375, D:D.375, D:E.377, J1V.29 ZN.38: 5 residues within 4Å: Chain E: D.295, K.302, D.375, E.377 Ligands: J1V.39 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Ligand interactions Metal complexes: E:D.295, E:D.375, E:D.375, E:E.377, J1V.39 ZN.47: 5 residues within 4Å: Chain F: D.295, K.302, D.375, E.377 Ligands: J1V.48 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Ligand interactions Metal complexes: F:D.295, F:D.375, F:D.375, F:E.377, J1V.48

6 x J1V: N-[(1R)-2-(hydroxyamino)-2-oxo-1-(3',4',5'-trifluoro[1,1'-biphenyl]-4-yl)ethyl]cyclohexanecarboxamide(Non-covalent)

J1V.3: 22 residues within 4Å: Chain A: K.290, D.295, K.302, G.306, M.308, L.311, M.312, F.314, D.315, N.373, D.375, A.376, E.377, L.403, T.404, G.405, L.408, A.493, F.499 Ligands: CO3.1, ZN.2, SO4.11 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.314, A:A.376 Hydrogen bonds: A:K.290, A:K.302, A:G.378, A:L.403, A:G.405 Halogen bonds: A:G.306 J1V.15: 20 residues within 4Å: Chain B: K.290, D.295, K.302, G.306, M.308, L.311, M.312, F.314, D.315, N.373, D.375, E.377, L.403, T.404, G.405, L.408, A.493, F.499 Ligands: CO3.13, ZN.14 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.314 Hydrogen bonds: B:K.290, B:K.302, B:D.375, B:E.377, B:L.403, B:G.405 J1V.22: 21 residues within 4Å: Chain C: K.290, D.295, K.302, G.306, M.308, L.311, M.312, F.314, D.315, N.373, D.375, E.377, T.402, L.403, T.404, G.405, L.408, A.493, F.499 Ligands: CO3.20, ZN.21 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:F.314 Hydrogen bonds: C:K.290, C:K.302, C:D.375, C:D.375, C:L.403, C:G.405 Water bridges: C:A.406 Halogen bonds: C:G.306 J1V.29: 22 residues within 4Å: Chain D: K.290, D.295, K.302, G.306, S.307, M.308, L.311, M.312, F.314, D.315, N.373, D.375, E.377, L.403, T.404, G.405, L.408, S.470, A.493, F.499 Ligands: CO3.27, ZN.28 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:F.314 Hydrogen bonds: D:K.290, D:K.302, D:D.375, D:L.403, D:G.405 Water bridges: D:A.406 J1V.39: 20 residues within 4Å: Chain E: K.290, D.295, K.302, G.306, S.307, M.308, M.312, F.314, D.315, N.373, D.375, E.377, L.403, T.404, G.405, L.408, A.493, F.499 Ligands: CO3.37, ZN.38 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:F.314 Hydrogen bonds: E:K.290, E:K.302, E:D.375, E:L.403, E:G.405 Halogen bonds: E:G.306 J1V.48: 20 residues within 4Å: Chain F: K.290, D.295, K.302, G.306, M.308, L.311, M.312, F.314, D.315, N.373, D.375, E.377, L.403, T.404, G.405, L.408, A.493, F.499 Ligands: CO3.46, ZN.47 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:F.314 Hydrogen bonds: F:K.290, F:K.302, F:D.375, F:G.378, F:L.403, F:G.405 Water bridges: F:A.406

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

SO4.4: 5 residues within 4Å: Chain A: I.17, E.18, Y.19, N.20 Ligands: 1PE.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.17, A:Y.19, A:N.20, A:N.20 SO4.5: 1 residues within 4Å: Chain A: K.27 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.27 SO4.8: 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, 2 interactions with chain B, 2 interactions with chain C Hydrogen bonds: A:K.352, B:K.352, C:K.352 Water bridges: A:K.352 Salt bridges: A:K.352, B:K.352, C:K.352 SO4.11: 4 residues within 4Å: Chain A: L.408, F.499 Chain F: K.468 Ligands: J1V.3 2 PLIP interactions: 2 interactions with chain F Water bridges: F:K.468 Salt bridges: F:K.468 SO4.12: 3 residues within 4Å: Chain A: R.502 Chain C: N.461, S.465 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:N.461, C:S.465, C:S.465 Water bridges: C:S.465, A:R.502 Salt bridges: A:R.502 SO4.19: 9 residues within 4Å: Chain B: F.72, N.77, M.78, K.80, F.91 Chain F: Y.92, M.93, F.94, S.100 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain B Hydrogen bonds: F:S.100 Salt bridges: B:K.80 SO4.26: 10 residues within 4Å: Chain C: F.72, N.77, M.78, K.80, F.81, F.91 Chain E: Y.92, M.93, F.94, S.100 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain E Hydrogen bonds: C:N.77, E:M.93, E:S.100 Water bridges: C:K.80 Salt bridges: C:K.80 SO4.30: 5 residues within 4Å: Chain D: I.17, E.18, Y.19, N.20 Ligands: 1PE.34 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Y.19, D:N.20, D:N.20 Water bridges: D:I.17 SO4.31: 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, 3 interactions with chain F, 2 interactions with chain D Hydrogen bonds: E:S.351, E:K.352, F:S.351, F:K.352, D:K.352 Salt bridges: E:K.352, F:K.352, D:K.352 SO4.44: 5 residues within 4Å: Chain E: S.2, E.3, V.4, T.13, N.228 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:S.2, E:V.4, E:N.228 Water bridges: E:T.13, E:T.13 SO4.45: 3 residues within 4Å: Chain E: L.239, E.240, Y.241 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:Y.241, E:Y.241 SO4.49: 5 residues within 4Å: Chain F: I.17, E.18, Y.19, N.20 Ligands: 1PE.51 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:Y.19, F:N.20, F:N.20, F:N.20

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

1PE.6: 5 residues within 4Å: Chain A: Y.19, N.20, K.236, L.237, Y.327 Ligand excluded by PLIP 1PE.7: 5 residues within 4Å: Chain A: Y.19, N.20, E.232, K.236 Ligands: SO4.4 Ligand excluded by PLIP 1PE.16: 7 residues within 4Å: Chain B: Y.19, H.24, F.205, K.236, L.237, Y.327 Ligands: 1PE.17 Ligand excluded by PLIP 1PE.17: 4 residues within 4Å: Chain B: Y.19, E.232, K.236 Ligands: 1PE.16 Ligand excluded by PLIP 1PE.23: 6 residues within 4Å: Chain C: Y.19, N.20, E.232, Q.235, K.236 Ligands: 1PE.24 Ligand excluded by PLIP 1PE.24: 7 residues within 4Å: Chain C: Y.19, N.20, H.24, F.205, K.236, Y.327 Ligands: 1PE.23 Ligand excluded by PLIP 1PE.32: 5 residues within 4Å: Chain D: Y.19, N.20, H.24, K.236, Y.327 Ligand excluded by PLIP 1PE.33: 6 residues within 4Å: Chain D: N.365, K.367, D.459, E.480, Q.483 Chain E: S.170 Ligand excluded by PLIP 1PE.34: 4 residues within 4Å: Chain D: Y.19, E.232, K.236 Ligands: SO4.30 Ligand excluded by PLIP 1PE.35: 5 residues within 4Å: Chain D: N.421, N.422, N.484, T.485, A.486 Ligand excluded by PLIP 1PE.40: 5 residues within 4Å: Chain E: Y.19, N.20, E.232, Q.235, K.236 Ligand excluded by PLIP 1PE.41: 7 residues within 4Å: Chain E: Y.19, N.20, H.24, F.205, K.236, L.237, Y.327 Ligand excluded by PLIP 1PE.42: 5 residues within 4Å: Chain E: N.365, K.367, D.459, E.480 Chain F: S.170 Ligand excluded by PLIP 1PE.50: 6 residues within 4Å: Chain F: Y.19, N.20, H.24, F.205, K.236, Y.327 Ligand excluded by PLIP 1PE.51: 6 residues within 4Å: Chain F: Y.19, N.20, E.232, Q.235, K.236 Ligands: SO4.49 Ligand excluded by PLIP 1PE.52: 5 residues within 4Å: Chain D: S.170 Chain F: N.365, K.367, D.459, Q.483 Ligand excluded by PLIP

6 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.9: 7 residues within 4Å: Chain A: L.130, H.131, D.132, N.133, Y.162, N.176, E.178 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:Y.179 DMS.10: 4 residues within 4Å: Chain A: E.41, G.42, L.135, S.136 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.42 DMS.18: 5 residues within 4Å: Chain B: N.421, N.422, N.484, T.485, A.486 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.422 DMS.25: 8 residues within 4Å: Chain C: L.130, H.131, D.132, N.133, Y.162, N.176, M.177, E.178 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.131, C:D.132 DMS.36: 5 residues within 4Å: Chain D: S.2, E.3, V.4, T.13, N.228 1 PLIP interactions: 1 interactions with chain D Water bridges: D:N.228 DMS.43: 5 residues within 4Å: Chain E: N.421, N.422, N.484, T.485, A.486 1 PLIP interactions: 1 interactions with chain E Water bridges: E:T.485

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vinh, N.B. et al., Hydroxamic Acid Inhibitors Provide Cross-Species Inhibition of Plasmodium M1 and M17 Aminopeptidases. J. Med. Chem. (2019)

Release Date

2018-12-26

Peptides

Pf-M17: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Pf-M17

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