SMTL ID : 5cbm.2 (1 other biounit)

Crystal structure of PfA-M17 with virtual ligand inhibitor

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: 8 residues within 4Å: Chain A: K.290, A.376, E.377, G.378, R.379, L.403 Ligands: ZN.2, 4ZN.4 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 CO3.12: 8 residues within 4Å: Chain B: K.290, A.376, E.377, G.378, R.379, L.403 Ligands: ZN.13, 4ZN.15 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.377, B:R.379, B:R.379 CO3.18: 8 residues within 4Å: Chain C: K.290, A.376, E.377, G.378, R.379, L.403 Ligands: ZN.19, 4ZN.21 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.379, C:R.379, C:L.403 CO3.26: 9 residues within 4Å: Chain D: K.290, D.375, A.376, E.377, G.378, R.379, L.403 Ligands: ZN.27, 4ZN.29 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:K.290, D:G.378, D:R.379, D:L.403 CO3.35: 8 residues within 4Å: Chain E: K.290, A.376, E.377, G.378, R.379, L.403 Ligands: ZN.36, 4ZN.38 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:E.377, E:G.378, E:R.379, E:R.379, E:R.379 CO3.43: 8 residues within 4Å: Chain F: K.290, A.376, E.377, G.378, R.379, L.403 Ligands: ZN.44, 4ZN.46 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:E.377, F:G.378, F:R.379, F:R.379, F:R.379

12 x ZN: ZINC ION(Non-covalent)

ZN.2: 7 residues within 4Å: Chain A: K.290, D.295, D.315, E.377 Ligands: CO3.1, ZN.3, 4ZN.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.295, A:D.315, A:D.315, A:E.377 ZN.3: 6 residues within 4Å: Chain A: D.295, K.302, D.375, E.377 Ligands: ZN.2, 4ZN.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.295, A:D.375, A:D.375, A:E.377 ZN.13: 7 residues within 4Å: Chain B: K.290, D.295, D.315, E.377 Ligands: CO3.12, ZN.14, 4ZN.15 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.295, B:D.315, B:E.377 ZN.14: 6 residues within 4Å: Chain B: D.295, K.302, D.375, E.377 Ligands: ZN.13, 4ZN.15 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.295, B:D.375, B:D.375, B:E.377 ZN.19: 7 residues within 4Å: Chain C: K.290, D.295, D.315, E.377 Ligands: CO3.18, ZN.20, 4ZN.21 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.295, C:D.315, C:E.377 ZN.20: 6 residues within 4Å: Chain C: D.295, K.302, D.375, E.377 Ligands: ZN.19, 4ZN.21 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.295, C:D.375, C:D.375, C:E.377 ZN.27: 7 residues within 4Å: Chain D: K.290, D.295, D.315, E.377 Ligands: CO3.26, ZN.28, 4ZN.29 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.295, D:D.315, D:E.377 ZN.28: 6 residues within 4Å: Chain D: D.295, K.302, D.375, E.377 Ligands: ZN.27, 4ZN.29 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.295, D:D.375, D:D.375, D:E.377 ZN.36: 7 residues within 4Å: Chain E: K.290, D.295, D.315, E.377 Ligands: CO3.35, ZN.37, 4ZN.38 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:D.295, E:D.315, E:E.377 ZN.37: 6 residues within 4Å: Chain E: D.295, K.302, D.375, E.377 Ligands: ZN.36, 4ZN.38 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.295, E:D.375, E:D.375, E:E.377 ZN.44: 7 residues within 4Å: Chain F: K.290, D.295, D.315, E.377 Ligands: CO3.43, ZN.45, 4ZN.46 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:D.295, F:D.315, F:E.377 ZN.45: 6 residues within 4Å: Chain F: D.295, K.302, D.375, E.377 Ligands: ZN.44, 4ZN.46 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.295, F:D.375, F:D.375, F:E.377

6 x 4ZN: (2S)-2-{[(R)-[(R)-amino(phenyl)methyl](hydroxy)phosphoryl]methyl}-4-methylpentanoic acid(Non-covalent)

4ZN.4: 16 residues within 4Å: Chain A: K.290, D.295, K.302, M.312, F.314, D.315, D.375, E.377, T.402, L.403, T.404, G.405, A.493 Ligands: CO3.1, ZN.2, ZN.3 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.314, A:A.493 Hydrogen bonds: A:K.302, A:D.315, A:G.405 Water bridges: A:A.406 Salt bridges: A:K.302 4ZN.15: 17 residues within 4Å: Chain B: K.290, D.295, K.302, M.308, M.312, F.314, D.315, D.375, E.377, T.402, L.403, T.404, G.405, A.493 Ligands: CO3.12, ZN.13, ZN.14 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:F.314, B:A.493 Hydrogen bonds: B:K.302, B:D.315, B:D.375, B:G.405, B:A.406 Water bridges: B:L.403 Salt bridges: B:K.302 4ZN.21: 16 residues within 4Å: Chain C: K.290, D.295, K.302, M.308, M.312, F.314, D.315, D.375, E.377, T.402, L.403, G.405, A.493 Ligands: CO3.18, ZN.19, ZN.20 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.314, C:A.493 Hydrogen bonds: C:K.302, C:D.315, C:D.375 4ZN.29: 18 residues within 4Å: Chain D: K.290, D.295, K.302, M.308, M.312, F.314, D.315, D.375, E.377, T.402, L.403, T.404, G.405, A.406, A.493 Ligands: CO3.26, ZN.27, ZN.28 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:F.314, D:A.493 Hydrogen bonds: D:K.302, D:D.315, D:D.375, D:L.403, D:G.405, D:A.406 Salt bridges: D:K.302 4ZN.38: 17 residues within 4Å: Chain E: K.290, D.295, K.302, M.308, M.312, F.314, D.315, D.375, E.377, T.402, L.403, T.404, G.405, A.493 Ligands: CO3.35, ZN.36, ZN.37 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:F.314, E:A.493 Hydrogen bonds: E:K.302, E:D.315 4ZN.46: 15 residues within 4Å: Chain F: K.290, D.295, K.302, F.314, D.315, D.375, E.377, T.402, L.403, T.404, G.405, A.493 Ligands: CO3.43, ZN.44, ZN.45 9 PLIP interactions: 9 interactions with chain F Hydrophobic interactions: F:F.314, F:A.493 Hydrogen bonds: F:K.290, F:K.302, F:D.315, F:D.375, F:G.405, F:A.406 Water bridges: F:S.470

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

1PE.5: 5 residues within 4Å: Chain A: Y.19, N.20, H.24, K.236, Y.327 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.331 1PE.6: 4 residues within 4Å: Chain A: Y.31, N.38, Y.186 Ligands: 1PE.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.31, A:N.38, A:Y.186 1PE.7: 2 residues within 4Å: Chain A: N.38 Ligands: 1PE.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.38 Water bridges: A:G.36 1PE.16: 3 residues within 4Å: Chain B: Y.19, E.232, K.236 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.19 Hydrogen bonds: B:K.236 1PE.17: 5 residues within 4Å: Chain B: Y.19, H.24, F.205, K.236, Y.327 No protein-ligand interaction detected (PLIP) 1PE.22: 5 residues within 4Å: Chain C: Y.19, E.232, Q.235, K.236 Ligands: SO4.24 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:K.236 Hydrogen bonds: C:K.236 1PE.23: 6 residues within 4Å: Chain C: Y.19, N.20, H.24, F.205, K.236, Y.327 No protein-ligand interaction detected (PLIP) 1PE.30: 5 residues within 4Å: Chain D: S.170 Chain F: N.365, K.367, D.459, Q.483 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:K.367, F:E.480 1PE.31: 4 residues within 4Å: Chain D: Y.19, E.232, Q.235, K.236 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.236 1PE.32: 5 residues within 4Å: Chain D: Y.19, N.20, H.24, K.236, Y.327 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.236 1PE.39: 5 residues within 4Å: Chain E: Y.19, E.232, Q.235, K.236 Ligands: SO4.41 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:Y.19, E:K.236 Hydrogen bonds: E:K.236 1PE.40: 3 residues within 4Å: Chain E: Y.19, K.236, Y.327 2 PLIP interactions: 2 interactions with chain E Water bridges: E:Y.327, E:Y.327 1PE.47: 8 residues within 4Å: Chain A: E.116, A.117, S.414, Y.415 Chain F: I.445, I.446, N.447, E.448 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain F Hydrogen bonds: A:E.116, A:S.414, F:I.445, F:N.447, F:N.447, F:E.448 Water bridges: A:S.115, A:E.116, A:Y.415 1PE.48: 6 residues within 4Å: Chain F: Y.19, N.20, H.24, F.205, K.236, Y.327 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:K.236 Water bridges: F:Y.327, F:Y.327

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

SO4.8: 4 residues within 4Å: Chain A: I.17, E.18, Y.19, N.20 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.19, A:N.20, A:N.20 SO4.9: 6 residues within 4Å: Chain A: S.351, K.352 Chain B: S.351, K.352 Chain C: S.351, K.352 6 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C, 2 interactions with chain B Hydrogen bonds: A:K.352, C:K.352, B:K.352 Salt bridges: A:K.352, C:K.352, B:K.352 SO4.10: 5 residues within 4Å: Chain A: G.42, K.134, L.135, S.136 Chain D: K.80 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain A Water bridges: D:K.80 Salt bridges: D:K.80 Hydrogen bonds: A:G.42, A:K.134, A:S.136 SO4.11: 6 residues within 4Å: Chain A: R.379, Q.462, I.463, S.464, S.470, V.473 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.464, A:S.464 Salt bridges: A:R.379 SO4.24: 5 residues within 4Å: Chain C: I.17, E.18, Y.19, N.20 Ligands: 1PE.22 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.19, C:N.20 SO4.25: 5 residues within 4Å: Chain C: E.41, G.42, L.135, S.136 Chain E: K.80 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain E Hydrogen bonds: C:G.42, C:S.136, C:K.137 Salt bridges: E:K.80 SO4.33: 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 F, 3 interactions with chain E, 2 interactions with chain D Hydrogen bonds: F:S.351, F:K.352, E:S.351, E:K.352, D:K.352 Salt bridges: F:K.352, E:K.352, D:K.352 SO4.34: 4 residues within 4Å: Chain D: I.17, E.18, Y.19, N.20 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Y.19, D:N.20, D:N.20 SO4.41: 5 residues within 4Å: Chain E: I.17, E.18, Y.19, N.20 Ligands: 1PE.39 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:Y.19, E:N.20 SO4.42: 5 residues within 4Å: Chain E: A.304, P.305, G.306, S.307, M.308 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:G.306, E:S.307, E:M.308 SO4.49: 3 residues within 4Å: Chain F: E.18, Y.19, N.20 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:Y.19, F:N.20, F:N.20, F:N.20

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ruggeri, C. et al., Identification and Validation of a Potent Dual Inhibitor of the P. falciparum M1 and M17 Aminopeptidases Using Virtual Screening. Plos One (2015)

Release Date

2015-10-07

Peptides

M17 family aminopeptidase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
I

D
J

E
K

F
L

M17 family aminopeptidase

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