SMTL ID : 5cbm.1 (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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.379, A:R.379, A:L.403 CO3.13: 9 residues within 4Å: Chain B: K.290, D.375, A.376, E.377, G.378, R.379, L.403 Ligands: ZN.14, 4ZN.16 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.290, B:G.378, B:R.379, B:L.403 CO3.20: 8 residues within 4Å: Chain C: K.290, A.376, E.377, G.378, R.379, L.403 Ligands: ZN.21, 4ZN.23 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.290, C:R.379, C:R.379 CO3.31: 9 residues within 4Å: Chain D: K.290, D.375, A.376, E.377, G.378, R.379, L.403 Ligands: ZN.32, 4ZN.34 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:K.290, D:G.378, D:R.379, D:L.403 CO3.38: 8 residues within 4Å: Chain E: K.290, A.376, E.377, G.378, R.379, L.403 Ligands: ZN.39, 4ZN.41 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 CO3.47: 8 residues within 4Å: Chain F: K.290, A.376, E.377, G.378, R.379, L.403 Ligands: ZN.48, 4ZN.50 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 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.295, 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.14: 7 residues within 4Å: Chain B: K.290, D.295, D.315, E.377 Ligands: CO3.13, ZN.15, 4ZN.16 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.295, B:D.315, B:E.377 ZN.15: 6 residues within 4Å: Chain B: D.295, K.302, D.375, E.377 Ligands: ZN.14, 4ZN.16 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.295, B:D.375, B:D.375, B:E.377 ZN.21: 7 residues within 4Å: Chain C: K.290, D.295, D.315, E.377 Ligands: CO3.20, ZN.22, 4ZN.23 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.295, C:D.315, C:E.377 ZN.22: 6 residues within 4Å: Chain C: D.295, K.302, D.375, E.377 Ligands: ZN.21, 4ZN.23 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.295, C:D.375, C:D.375, C:E.377 ZN.32: 7 residues within 4Å: Chain D: K.290, D.295, D.315, E.377 Ligands: CO3.31, ZN.33, 4ZN.34 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.295, D:D.315, D:D.315, D:E.377 ZN.33: 6 residues within 4Å: Chain D: D.295, K.302, D.375, E.377 Ligands: ZN.32, 4ZN.34 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.295, D:D.375, D:D.375, D:E.377 ZN.39: 7 residues within 4Å: Chain E: K.290, D.295, D.315, E.377 Ligands: CO3.38, ZN.40, 4ZN.41 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.295, E:D.315, E:D.315, E:E.377 ZN.40: 6 residues within 4Å: Chain E: D.295, K.302, D.375, E.377 Ligands: ZN.39, 4ZN.41 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.295, E:D.375, E:D.375, E:E.377 ZN.48: 7 residues within 4Å: Chain F: K.290, D.295, D.315, E.377 Ligands: CO3.47, ZN.49, 4ZN.50 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:D.295, F:D.315, F:E.377 ZN.49: 6 residues within 4Å: Chain F: D.295, K.302, D.375, E.377 Ligands: ZN.48, 4ZN.50 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:D.295, 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: 17 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.406, A.493 Ligands: CO3.1, ZN.2, ZN.3 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.314, A:A.493 Hydrogen bonds: A:K.302, A:D.315, A:G.405, A:A.406 4ZN.16: 15 residues within 4Å: Chain B: K.290, D.295, K.302, M.312, F.314, D.315, D.375, E.377, T.402, L.403, G.405, A.493 Ligands: CO3.13, ZN.14, ZN.15 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.314, B:A.493 Hydrogen bonds: B:D.315 Water bridges: B:N.373, B:R.379, B:R.379, B:R.379 Salt bridges: B:K.302 4ZN.23: 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: CO3.20, ZN.21, ZN.22 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:F.314, C:A.493 Hydrogen bonds: C:K.290, C:K.302, C:D.315, C:D.375, C:G.405 Water bridges: C:L.403, C:A.406 Salt bridges: C:K.302 4ZN.34: 19 residues within 4Å: Chain D: K.290, D.295, K.302, M.308, M.312, F.314, D.315, D.375, E.377, R.379, T.402, L.403, T.404, G.405, S.470, A.493 Ligands: CO3.31, ZN.32, ZN.33 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:F.314, D:A.493 Hydrogen bonds: D:K.302, D:D.315, D:D.375, D:G.405, D:S.470 Water bridges: D:R.379, D:R.379 Salt bridges: D:R.379 4ZN.41: 18 residues within 4Å: Chain E: K.290, D.295, K.302, M.312, F.314, D.315, D.375, A.376, E.377, T.402, L.403, T.404, G.405, A.406, A.493 Ligands: CO3.38, ZN.39, ZN.40 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:F.314, E:A.376, E:A.493 Hydrogen bonds: E:K.302, E:D.315, E:L.403, E:G.405, E:A.406 4ZN.50: 17 residues within 4Å: Chain F: 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: CO3.47, ZN.48, ZN.49 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:F.314, F:A.493 Hydrogen bonds: F:K.302, F:D.315, F:G.405 Water bridges: F:A.406, F:A.406 Salt bridges: F:K.302

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

1PE.5: 5 residues within 4Å: Chain A: Y.19, N.20, H.24, L.237, Y.327 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.236 1PE.6: 4 residues within 4Å: Chain A: Y.19, E.232, K.236 Ligands: SO4.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.236 1PE.17: 6 residues within 4Å: Chain B: Y.19, N.20, H.24, K.236, Y.327 Ligands: 1PE.18 No protein-ligand interaction detected (PLIP) 1PE.18: 4 residues within 4Å: Chain B: Y.19, E.232, K.236 Ligands: 1PE.17 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:K.236 Hydrogen bonds: B:K.236 1PE.24: 4 residues within 4Å: Chain C: Y.19, E.232, Q.235, K.236 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:Q.235, C:K.236 Hydrogen bonds: C:K.236 1PE.25: 7 residues within 4Å: Chain C: Y.19, N.20, H.24, F.205, K.236, L.237, Y.327 No protein-ligand interaction detected (PLIP) 1PE.35: 4 residues within 4Å: Chain D: Y.19, E.232, K.236 Ligands: SO4.37 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:K.236 Hydrogen bonds: D:K.236 1PE.36: 6 residues within 4Å: Chain D: Y.19, N.20, H.24, F.205, K.236, Y.327 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Y.327 1PE.42: 6 residues within 4Å: Chain E: Y.19, E.232, Q.235, K.236 Ligands: 1PE.43, SO4.45 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:K.236 Hydrogen bonds: E:K.236 1PE.43: 5 residues within 4Å: Chain E: Y.19, F.205, K.236, Y.327 Ligands: 1PE.42 2 PLIP interactions: 2 interactions with chain E Water bridges: E:Y.327, E:Y.327 1PE.51: 6 residues within 4Å: Chain F: Y.19, H.24, F.205, K.236, L.237, Y.327 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 5 residues within 4Å: Chain A: N.421, N.422, N.484, T.485, A.486 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.422 Water bridges: A:A.486, A:A.486

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

SO4.8: 4 residues within 4Å: Chain A: E.18, Y.19, N.20 Ligands: 1PE.6 Ligand excluded by PLIP SO4.9: 4 residues within 4Å: Chain A: P.305, G.306, S.307, M.308 Ligand excluded by PLIP SO4.10: 6 residues within 4Å: Chain A: E.41, G.42, K.134, L.135, S.136 Chain D: K.80 Ligand excluded by PLIP SO4.11: 4 residues within 4Å: Chain A: M.308, L.408, F.499 Chain F: K.468 Ligand excluded by PLIP SO4.12: 6 residues within 4Å: Chain A: R.379, Q.462, I.463, S.464, S.470, V.473 Ligand excluded by PLIP SO4.19: 6 residues within 4Å: Chain A: S.351, K.352 Chain B: S.351, K.352 Chain C: S.351, K.352 Ligand excluded by PLIP SO4.26: 3 residues within 4Å: Chain C: E.18, Y.19, N.20 Ligand excluded by PLIP SO4.27: 5 residues within 4Å: Chain C: A.304, P.305, G.306, S.307, M.308 Ligand excluded by PLIP SO4.28: 4 residues within 4Å: Chain C: M.308, L.408, F.499 Chain D: K.468 Ligand excluded by PLIP SO4.29: 6 residues within 4Å: Chain C: I.445, I.446, N.447, E.448 Chain D: E.116, Y.415 Ligand excluded by PLIP SO4.30: 7 residues within 4Å: Chain C: R.379, Q.462, I.463, S.464, V.467, S.470, V.473 Ligand excluded by PLIP SO4.37: 5 residues within 4Å: Chain D: I.17, E.18, Y.19, N.20 Ligands: 1PE.35 Ligand excluded by PLIP SO4.44: 6 residues within 4Å: Chain D: S.351, K.352 Chain E: S.351, K.352 Chain F: S.351, K.352 Ligand excluded by PLIP SO4.45: 5 residues within 4Å: Chain E: I.17, E.18, Y.19, N.20 Ligands: 1PE.42 Ligand excluded by PLIP SO4.46: 4 residues within 4Å: Chain E: H.131, Y.162, E.178, Y.179 Ligand excluded by PLIP SO4.52: 3 residues within 4Å: Chain F: E.18, Y.19, N.20 Ligand excluded by PLIP SO4.53: 5 residues within 4Å: Chain F: L.130, H.131, Y.162, E.178, Y.179 Ligand excluded by PLIP

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
A

B
B

C
C

D
D

E
E

F
F

M17 family aminopeptidase

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