SMTL ID : 7sxq.2 (1 other biounit)

Plasmodium falciparum apicoplast DNA polymerase (exo-minus) without affinity tag

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 5 residues within 4Å: Chain A: E.426, L.429, K.430, N.433, K.611 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.430 Water bridges: A:N.433

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 8 residues within 4Å: Chain A: I.237, D.240, I.241, K.244, L.557, V.560, D.561, Y.607 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.244 Water bridges: A:Y.607 PEG.3: 6 residues within 4Å: Chain A: I.422, S.525, T.526, L.527, N.529, P.546 No protein-ligand interaction detected (PLIP)

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 7 residues within 4Å: Chain A: F.411, K.412, Q.413, I.414, K.417, C.614, E.615 Ligand excluded by PLIP CL.5: 5 residues within 4Å: Chain A: F.158, K.227, I.230, H.236, N.239 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: N.234, N.529, K.531 Ligand excluded by PLIP

1 x NA: SODIUM ION(Non-functional Binders)

NA.7: 5 residues within 4Å: Chain A: N.82, I.83, I.137, Q.138, D.143 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.138, A:D.143

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chheda, P.R. et al., Promising antimalarials targeting apicoplast DNA polymerase from Plasmodium falciparum. Eur.J.Med.Chem. (2022)

Release Date

2022-10-19

Peptides

Apicoplast DNA polymerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Apicoplast DNA polymerase

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