SMTL ID : 8sw9.1 (1 other biounit)

Plasmodium falciparum M17 (A460S) mutant

Coordinates

PDB Format Compare

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: D.296, K.303, D.376, E.378 Ligands: ZN.2, 1PE.7 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.296, A:D.376, A:D.376, A:E.378 ZN.2: 8 residues within 4Å: Chain A: K.291, I.293, D.296, D.316, E.378 Ligands: ZN.1, CO3.3, 1PE.7 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.296, A:D.316, A:E.378 ZN.9: 6 residues within 4Å: Chain B: D.296, G.298, K.303, D.376, E.378 Ligands: ZN.10 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.296, B:D.296, B:D.376, B:D.376, B:E.378 ZN.10: 8 residues within 4Å: Chain B: K.291, I.293, D.296, D.316, E.378, G.379 Ligands: CO3.8, ZN.9 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.296, B:D.316, B:E.378 ZN.13: 8 residues within 4Å: Chain C: K.291, I.293, D.296, D.316, E.378 Ligands: ZN.14, CO3.15, 1PE.19 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.296, C:D.316, C:D.316, C:E.378 ZN.14: 6 residues within 4Å: Chain C: D.296, K.303, N.349, D.376, E.378 Ligands: ZN.13 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.296, C:D.376, C:D.376, C:E.378 ZN.21: 7 residues within 4Å: Chain D: D.296, G.298, K.303, D.376, E.378 Ligands: ZN.22, 1PE.27 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.296, D:D.376, D:D.376, D:E.378 ZN.22: 9 residues within 4Å: Chain D: K.291, I.293, D.296, D.316, E.378, G.379 Ligands: ZN.21, CO3.23, 1PE.27 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.296, D:D.316, D:E.378 ZN.28: 9 residues within 4Å: Chain E: K.291, I.293, D.296, D.316, E.378, G.379 Ligands: ZN.29, CO3.30, 1PE.33 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:D.296, E:D.316, E:E.378 ZN.29: 8 residues within 4Å: Chain E: K.291, D.296, G.298, K.303, D.376, E.378 Ligands: ZN.28, 1PE.33 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.296, E:D.376, E:D.376, E:E.378 ZN.35: 8 residues within 4Å: Chain F: D.296, G.298, K.303, N.349, D.376, E.378 Ligands: ZN.36, 1PE.38 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.296, F:D.376, F:D.376, F:E.378 ZN.36: 9 residues within 4Å: Chain F: K.291, I.293, D.296, D.316, E.378, G.379 Ligands: ZN.35, CO3.37, 1PE.38 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:D.296, F:D.316, F:E.378

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

CO3.3: 9 residues within 4Å: Chain A: K.291, D.376, S.377, E.378, G.379, R.380, L.404, T.405 Ligands: ZN.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.291, A:S.377, A:G.379, A:L.404 CO3.8: 9 residues within 4Å: Chain B: K.291, D.376, S.377, E.378, G.379, R.380, L.404, T.405 Ligands: ZN.10 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.378, B:G.379, B:R.380, B:R.380 CO3.15: 9 residues within 4Å: Chain C: K.291, D.376, S.377, E.378, G.379, R.380, L.404, T.405 Ligands: ZN.13 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.291, C:D.376, C:G.379, C:R.380 CO3.23: 9 residues within 4Å: Chain D: K.291, D.376, S.377, E.378, G.379, R.380, L.404, T.405 Ligands: ZN.22 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.380, D:R.380, D:L.404 CO3.30: 9 residues within 4Å: Chain E: K.291, D.376, S.377, E.378, G.379, R.380, L.404, T.405 Ligands: ZN.28 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:K.291, E:G.379, E:R.380, E:L.404 CO3.37: 8 residues within 4Å: Chain F: K.291, D.376, S.377, E.378, G.379, R.380, L.404 Ligands: ZN.36 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:R.380, F:R.380, F:L.404

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

SO4.4: 8 residues within 4Å: Chain A: Y.161, D.166, Y.209, S.212, A.216, K.504, P.505 Chain C: Y.458 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:D.166, A:D.166, A:S.212, C:Y.458, C:Y.458 Salt bridges: A:K.504 SO4.5: 7 residues within 4Å: Chain A: I.447, N.448, E.449 Chain F: S.116, E.117, A.118, Y.416 8 PLIP interactions: 4 interactions with chain F, 4 interactions with chain A Hydrogen bonds: F:E.117, F:E.117, F:Y.416, A:N.448, A:N.448, A:E.449 Water bridges: F:S.116, A:E.449 SO4.11: 6 residues within 4Å: Chain A: S.352, K.353 Chain B: S.352, K.353 Chain C: S.352, K.353 10 PLIP interactions: 4 interactions with chain B, 4 interactions with chain C, 2 interactions with chain A Hydrogen bonds: B:S.352, B:S.352, B:K.353, C:S.352, C:S.352, C:K.353, A:S.352, A:K.353 Salt bridges: B:K.353, C:K.353 SO4.16: 7 residues within 4Å: Chain C: E.42, G.43, K.135, L.136, S.137, K.138 Chain E: K.81 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 SO4.20: 5 residues within 4Å: Chain C: P.306, G.307, S.308, M.309, I.310 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:G.307, C:S.308, C:S.308, C:S.308, C:M.309 Water bridges: C:I.310 SO4.24: 7 residues within 4Å: Chain A: F.73, F.82 Chain D: Y.93, M.94, F.95, S.101, V.102 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:M.94, D:M.94, D:S.101, D:V.102 SO4.31: 6 residues within 4Å: Chain C: F.73, N.78, K.81 Chain E: Y.93, F.95, S.101 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain E Hydrogen bonds: C:N.78, E:S.101 Salt bridges: C:K.81 SO4.34: 6 residues within 4Å: Chain D: S.352, K.353 Chain E: S.352, K.353 Chain F: S.352, K.353 7 PLIP interactions: 2 interactions with chain E, 2 interactions with chain D, 3 interactions with chain F Hydrogen bonds: E:S.352, E:K.353, D:S.352, D:K.353, F:S.352, F:K.353 Salt bridges: F:K.353

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

1PE.6: 7 residues within 4Å: Chain A: Y.20, N.21, H.25, F.206, K.237, L.238, Y.328 No protein-ligand interaction detected (PLIP) 1PE.7: 17 residues within 4Å: Chain A: K.291, D.296, K.303, G.307, S.308, M.309, M.313, F.315, D.316, T.403, L.404, T.405, G.406, L.409, A.494 Ligands: ZN.1, ZN.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.303 Water bridges: A:Y.410 1PE.12: 7 residues within 4Å: Chain B: Y.20, H.25, F.206, L.234, K.237, L.238, Y.328 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:K.237, B:L.238 1PE.17: 6 residues within 4Å: Chain C: Y.20, N.21, E.233, Q.236, K.237 Ligands: 1PE.18 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:K.237 Hydrogen bonds: C:K.237 1PE.18: 8 residues within 4Å: Chain C: Y.20, N.21, H.25, F.206, K.237, L.238, Y.328 Ligands: 1PE.17 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.328 1PE.19: 16 residues within 4Å: Chain C: K.291, D.296, K.303, G.307, S.308, M.309, M.313, F.315, D.316, T.403, L.404, G.406, L.409, Y.410, A.494 Ligands: ZN.13 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.303, C:D.316 1PE.25: 9 residues within 4Å: Chain D: Y.20, N.21, H.25, F.206, L.234, K.237, L.238, Y.328 Ligands: 1PE.26 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Y.328 1PE.26: 4 residues within 4Å: Chain D: Y.20, E.233, K.237 Ligands: 1PE.25 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.237 1PE.27: 16 residues within 4Å: Chain D: K.291, D.296, K.303, G.307, S.308, M.313, F.315, D.316, T.403, L.404, T.405, G.406, L.409, A.494 Ligands: ZN.21, ZN.22 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.303, D:D.316 1PE.32: 7 residues within 4Å: Chain E: Y.20, N.21, H.25, F.206, K.237, L.238, Y.328 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:K.237, E:Y.328 1PE.33: 17 residues within 4Å: Chain E: K.291, D.296, K.303, G.307, S.308, M.309, M.313, F.315, D.316, D.376, T.403, L.404, G.406, L.409, A.494 Ligands: ZN.28, ZN.29 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:D.296, E:K.303 1PE.38: 17 residues within 4Å: Chain F: K.291, D.296, K.303, G.307, S.308, M.309, M.313, F.315, D.316, T.403, L.404, T.405, G.406, L.409, A.494 Ligands: ZN.35, ZN.36 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:K.303, F:G.307

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

de Koning-Ward, T.F. et al., Characterisation of a novel antimalarial agent targeting haemaglobin digestion that shows cross-species reactivity and excellent in vivo properties. Mbio (2024)

Release Date

2024-04-24

Peptides

Leucine aminopeptidase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Leucine aminopeptidase

Related Entries With Identical Sequence