SMTL ID : 6jwz.1

Crystal structure of Plasmodium falciparum HPPK-DHPS S436F/A437G/A613S triple mutant with SDX-DHP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.95 Å

Oligo State

homo-dimer

Ligands

2 x CKL: 4-[(2-azanyl-4-oxidanylidene-7,8-dihydro-3~{H}-pteridin-6-yl)methylamino]-~{N}-(5,6-dimethoxypyrimidin-4-yl)benzenesulfonamide(Non-covalent)

CKL.1: 16 residues within 4Å: Chain A: D.482, N.502, I.504, V.527, M.529, P.535, D.539, D.575, G.579, F.580, F.603, G.605, K.609, R.610, R.686 Ligands: PO4.2 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.580, A:K.609 Hydrogen bonds: A:N.502, A:N.502, A:G.605, A:K.609, A:R.610 Water bridges: A:D.575, A:G.605, A:R.686 Salt bridges: A:D.482, A:D.575 pi-Cation interactions: A:R.610, A:R.686 CKL.9: 16 residues within 4Å: Chain B: F.436, D.482, N.502, I.504, V.527, M.529, D.539, D.575, G.579, F.580, F.603, G.605, K.609, R.610, R.686 Ligands: PO4.10 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:F.580, B:K.609 Hydrogen bonds: B:D.482, B:N.502, B:N.502, B:K.609, B:R.610, B:R.610 Water bridges: B:L.578, B:G.605, B:F.611 Salt bridges: B:D.575 pi-Cation interactions: B:R.686

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 5 residues within 4Å: Chain A: I.394, N.396, R.686, H.688 Ligands: CKL.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.396 Water bridges: A:R.686, A:R.686 Salt bridges: A:R.686, A:H.688 PO4.10: 3 residues within 4Å: Chain B: R.686, H.688 Ligands: CKL.9 5 PLIP interactions: 5 interactions with chain B Water bridges: B:S.607, B:R.686, B:R.686 Salt bridges: B:R.686, B:H.688

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.3: 14 residues within 4Å: Chain A: L.181, K.185, D.208, D.210, I.211, N.312, I.313, E.314, F.315, L.316, S.317, I.318, H.320 Ligands: MG.4 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:D.208, A:D.208, A:I.211, A:N.312, A:E.314, A:F.315, A:S.317, A:S.317 Salt bridges: A:K.185 pi-Stacking: A:F.315, A:H.320 AMP.11: 12 residues within 4Å: Chain B: L.181, D.208, D.210, I.211, N.312, I.313, E.314, F.315, L.316, S.317, H.320 Ligands: MG.12 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:D.208, B:I.211, B:N.312, B:E.314, B:F.315, B:S.317, B:S.317 Salt bridges: B:K.185 pi-Stacking: B:F.315

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: D.208, D.210 Ligands: AMP.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.208, A:D.208, A:D.210, AMP.3 MG.12: 3 residues within 4Å: Chain B: D.208, D.210 Ligands: AMP.11 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:D.208, B:D.208, B:D.210, AMP.11

2 x CA: CALCIUM ION(Non-covalent)

CA.5: 3 residues within 4Å: Chain A: E.42, G.46, E.99 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.42, A:G.46, A:E.99, A:E.99, H2O.3 CA.13: 4 residues within 4Å: Chain B: E.42, G.46, K.47, E.99 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.42, B:E.42, B:G.46, B:E.99, H2O.6

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.6: 4 residues within 4Å: Chain A: H.530, R.532, Y.544, Y.554 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.554 Salt bridges: A:H.530, A:R.532 ACT.14: 4 residues within 4Å: Chain B: H.530, R.532, Y.544, Y.554 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.554 Salt bridges: B:H.530, B:R.532

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

PEG.7: 4 residues within 4Å: Chain A: Y.676, Y.679, K.680 Ligands: PEG.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.680 PEG.8: 7 residues within 4Å: Chain A: Y.679, D.704 Chain B: Q.592, Y.676, Y.679, K.680 Ligands: PEG.7 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.592

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chitnumsub, P. et al., The structure of Plasmodium falciparum hydroxymethyldihydropterin pyrophosphokinase-dihydropteroate synthase reveals the basis of sulfa resistance. Febs J. (2020)

Release Date

2020-02-12

Peptides

7,8-dihydro-6-hydroxymethylpterin pyrophosphokinase-dihydropteroate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

7,8-dihydro-6-hydroxymethylpterin pyrophosphokinase-dihydropteroate synthase

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