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

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

monomer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 9 residues within 4Å: Chain A: F.40, E.41, F.58, I.59, I.60, N.64, Y.65, N.66, I.69 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.41, A:E.41, A:E.41, A:I.59, A:N.66, A:N.66

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

NA.2: 6 residues within 4Å: Chain A: N.82, I.83, I.137, Q.138, N.139, D.143 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.82, A:Q.138

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

CL.3: 3 residues within 4Å: Chain A: N.234, N.529, K.531 Ligand excluded by PLIP 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: 4 residues within 4Å: Chain A: Q.138, N.139, K.177, L.178 Ligand excluded by PLIP

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

PEG.7: 9 residues within 4Å: Chain A: H.236, 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:D.240, A:D.240 PEG.8: 6 residues within 4Å: Chain A: I.422, W.512, S.525, T.526, L.527, P.546 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.525, A:S.525

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

EDO.9: 4 residues within 4Å: Chain A: L.429, K.430, N.433, K.611 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.433

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

2022-10-26

Peptides

Plastid replication-repair enzyme: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Plastid replication-repair enzyme

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