SMTL ID : 4r6t.1 (1 other biounit)

Structure of the m17 leucyl aminopeptidase from malaria complexed with a hydroxamic acid-based inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-hexamer

Ligands

12 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: K.291, D.296, D.316, E.378 Ligands: ZN.3, R5T.7 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.296, A:D.316, A:E.378, H2O.2 ZN.3: 5 residues within 4Å: Chain A: D.296, D.376, E.378 Ligands: ZN.1, R5T.7 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.296, A:D.376, A:D.376, A:E.378, R5T.7 ZN.10: 6 residues within 4Å: Chain B: K.291, D.296, D.316, E.378 Ligands: ZN.12, R5T.15 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.296, B:D.316, B:E.378, H2O.8 ZN.12: 5 residues within 4Å: Chain B: D.296, D.376, E.378 Ligands: ZN.10, R5T.15 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:D.296, B:D.376, B:D.376, B:E.378, R5T.15 ZN.18: 6 residues within 4Å: Chain C: K.291, D.296, D.316, E.378 Ligands: ZN.20, R5T.24 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.296, C:D.316, C:E.378, H2O.16 ZN.20: 6 residues within 4Å: Chain C: D.296, K.303, D.376, E.378 Ligands: ZN.18, R5T.24 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:D.296, C:D.376, C:D.376, C:E.378, R5T.24 ZN.28: 7 residues within 4Å: Chain D: K.291, D.296, D.316, E.378 Ligands: CO3.29, ZN.30, R5T.31 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.296, D:D.316, D:D.316, D:E.378 ZN.30: 6 residues within 4Å: Chain D: D.296, K.303, D.376, E.378 Ligands: ZN.28, R5T.31 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.296, D:D.376, D:D.376, D:E.378 ZN.33: 6 residues within 4Å: Chain E: K.291, D.296, D.316, E.378 Ligands: ZN.35, R5T.36 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:D.296, E:D.316, E:E.378 ZN.35: 6 residues within 4Å: Chain E: D.296, K.303, D.376, E.378 Ligands: ZN.33, R5T.36 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Ligand interactions Metal complexes: E:D.296, E:D.376, E:D.376, E:E.378, R5T.36 ZN.41: 6 residues within 4Å: Chain F: K.291, D.296, D.316, E.378 Ligands: ZN.43, R5T.45 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.296, F:D.316, F:E.378, H2O.32 ZN.43: 6 residues within 4Å: Chain F: D.296, K.303, D.376, E.378 Ligands: ZN.41, R5T.45 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Ligand interactions Metal complexes: F:D.296, F:D.376, F:D.376, F:E.378, R5T.45

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

CO3.2: 7 residues within 4Å: Chain A: K.291, A.377, E.378, G.379, R.380, L.404 Ligands: R5T.7 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.291, A:A.377, A:G.379, A:R.380, A:L.404 CO3.11: 6 residues within 4Å: Chain B: K.291, A.377, G.379, R.380, L.404 Ligands: R5T.15 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.380, B:R.380, B:R.380 CO3.19: 7 residues within 4Å: Chain C: K.291, A.377, G.379, R.380, L.404, T.405 Ligands: R5T.24 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:A.377, C:G.379, C:R.380, C:L.404 CO3.29: 8 residues within 4Å: Chain D: K.291, A.377, E.378, G.379, R.380, L.404 Ligands: ZN.28, R5T.31 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.380, D:R.380, D:L.404 CO3.34: 7 residues within 4Å: Chain E: K.291, A.377, E.378, G.379, R.380, L.404 Ligands: R5T.36 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:R.380, E:R.380, E:L.404 CO3.42: 7 residues within 4Å: Chain F: K.291, A.377, E.378, G.379, R.380, L.404 Ligands: R5T.45 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:K.291, F:R.380, F:R.380

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

SO4.4: 7 residues within 4Å: Chain A: E.42, G.43, K.135, L.136, S.137, K.138 Chain D: K.81 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:G.43, A:S.137, A:K.138 Salt bridges: D:K.81 SO4.5: 4 residues within 4Å: Chain A: I.18, E.19, Y.20, N.21 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.20, A:N.21 SO4.6: 4 residues within 4Å: Chain A: P.306, G.307, S.308, M.309 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.307, A:S.308, A:M.309 Water bridges: A:I.310, A:I.310 SO4.9: 7 residues within 4Å: Chain A: Y.161, D.166, Y.209, S.212, K.504, P.505 Chain C: Y.458 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.166, A:D.166, A:S.212, A:S.212 SO4.13: 6 residues within 4Å: Chain A: S.352, K.353 Chain B: S.352, K.353 Chain C: S.352, K.353 8 PLIP interactions: 3 interactions with chain B, 3 interactions with chain C, 2 interactions with chain A Hydrogen bonds: B:S.352, B:K.353, C:S.352, C:K.353, A:K.353 Salt bridges: B:K.353, C:K.353, A:K.353 SO4.14: 3 residues within 4Å: Chain B: G.307, S.308, M.309 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.307, B:S.308, B:M.309, B:D.311 SO4.21: 4 residues within 4Å: Chain C: E.19, Y.20, N.21 Ligands: 1PE.25 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.20, C:N.21, C:N.21 SO4.22: 7 residues within 4Å: Chain C: F.73, K.81, F.82 Chain E: Y.93, M.94, F.95, S.101 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:K.81 SO4.23: 4 residues within 4Å: Chain C: G.43, K.135, L.136, S.137 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain E Hydrogen bonds: C:G.43, C:S.137 Salt bridges: E:K.81 SO4.40: 4 residues within 4Å: Chain E: I.18, Y.20, N.21 Ligands: 1PE.38 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:Y.20, E:N.21 SO4.44: 6 residues within 4Å: Chain D: S.352, K.353 Chain E: S.352, K.353 Chain F: S.352, K.353 4 PLIP interactions: 2 interactions with chain F, 1 interactions with chain D, 1 interactions with chain E Hydrogen bonds: F:K.353, D:K.353, E:K.353 Salt bridges: F:K.353 SO4.48: 4 residues within 4Å: Chain F: I.18, E.19, Y.20, N.21 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:Y.20, F:N.21, F:N.21

6 x R5T: tert-butyl {(1S)-2-(hydroxyamino)-2-oxo-1-[4-(1H-pyrazol-1-yl)phenyl]ethyl}carbamate(Non-covalent)

R5T.7: 17 residues within 4Å: Chain A: K.291, D.296, K.303, M.309, F.315, D.376, A.377, E.378, L.404, T.405, G.406, L.409, S.471, A.494 Ligands: ZN.1, CO3.2, ZN.3 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.377, A:L.409 Hydrogen bonds: A:K.291, A:K.303, A:E.378, A:L.404, A:L.404, A:G.406 R5T.15: 17 residues within 4Å: Chain B: K.291, D.296, K.303, F.315, D.376, A.377, E.378, G.379, R.380, L.404, G.406, L.409, S.471, A.494 Ligands: ZN.10, CO3.11, ZN.12 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:A.377, B:L.409 Hydrogen bonds: B:K.303, B:G.379, B:L.404, B:L.404 R5T.24: 21 residues within 4Å: Chain C: K.291, D.296, K.303, M.309, M.313, F.315, N.374, D.376, A.377, E.378, R.380, L.404, T.405, G.406, L.409, I.464, S.471, A.494 Ligands: ZN.18, CO3.19, ZN.20 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:A.377, C:L.409, C:I.464 Hydrogen bonds: C:K.291, C:K.303, C:E.378, C:L.404, C:L.404 R5T.31: 18 residues within 4Å: Chain D: K.291, D.296, K.303, M.313, F.315, N.374, D.376, A.377, E.378, R.380, L.404, T.405, G.406, S.471, A.494 Ligands: ZN.28, CO3.29, ZN.30 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:K.291, D:K.303, D:K.303, D:D.376, D:L.404, D:G.406, D:S.471 R5T.36: 18 residues within 4Å: Chain E: K.291, D.296, K.303, F.315, N.374, D.376, A.377, E.378, R.380, L.404, T.405, G.406, L.409, S.471, A.494 Ligands: ZN.33, CO3.34, ZN.35 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:A.377, E:L.409 Hydrogen bonds: E:K.303, E:R.380, E:L.404, E:L.404, E:G.406 Water bridges: E:S.471 R5T.45: 16 residues within 4Å: Chain F: K.291, D.296, K.303, M.309, D.376, A.377, E.378, R.380, L.404, T.405, G.406, L.409, A.494 Ligands: ZN.41, CO3.42, ZN.43 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:A.377, F:L.409 Hydrogen bonds: F:K.303, F:L.404, F:L.404

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

1PE.8: 6 residues within 4Å: Chain A: Y.20, N.21, H.25, F.206, K.237, Y.328 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.328 1PE.16: 4 residues within 4Å: Chain B: Y.20, E.233, K.237 Ligands: 1PE.17 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.233 1PE.17: 7 residues within 4Å: Chain B: Y.20, N.21, H.25, F.206, K.237, Y.328 Ligands: 1PE.16 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.237 Water bridges: B:Y.328, B:Y.328 1PE.25: 6 residues within 4Å: Chain C: Y.20, N.21, E.233, K.237 Ligands: SO4.21, 1PE.26 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:E.233 Hydrogen bonds: C:K.237 1PE.26: 7 residues within 4Å: Chain C: Y.20, N.21, H.25, F.206, K.237, Y.328 Ligands: 1PE.25 No protein-ligand interaction detected (PLIP) 1PE.27: 8 residues within 4Å: Chain C: I.446, I.447, N.448, E.449 Chain D: E.117, A.118, S.415, Y.416 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:N.448, C:N.448, C:E.449, D:S.415 Water bridges: C:E.449, C:E.449 1PE.32: 6 residues within 4Å: Chain D: N.21, H.25, F.206, K.237, L.238, Y.328 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.237 1PE.37: 7 residues within 4Å: Chain E: Y.20, N.21, H.25, F.206, K.237, Y.328 Ligands: 1PE.38 No protein-ligand interaction detected (PLIP) 1PE.38: 5 residues within 4Å: Chain E: Y.20, E.233, K.237 Ligands: 1PE.37, SO4.40 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:E.233, E:K.237 1PE.39: 3 residues within 4Å: Chain E: S.434, K.435, V.441 No protein-ligand interaction detected (PLIP) 1PE.46: 6 residues within 4Å: Chain F: Y.20, N.21, F.206, K.237, L.238, Y.328 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:K.237, F:L.238 1PE.47: 6 residues within 4Å: Chain F: S.10, L.11, D.12, P.13, T.14, Y.221 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mistry, S.N. et al., Two-Pronged Attack: Dual Inhibition of Plasmodium falciparum M1 and M17 Metalloaminopeptidases by a Novel Series of Hydroxamic Acid-Based Inhibitors. J.Med.Chem. (2014)

Release Date

2014-10-29

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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