SMTL ID : 6jwy.1

Crystal structure of Plasmodium falciparum HPPK-DHPS A437G with SDX-DHP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 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: 15 residues within 4Å: Chain A: 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: ACT.8 13 PLIP interactions: 13 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:F.611 Salt bridges: A:D.482, A:D.575 pi-Cation interactions: A:R.686 CKL.9: 17 residues within 4Å: Chain B: D.482, N.502, I.504, V.527, M.529, P.535, M.538, D.539, D.575, G.579, F.580, F.603, G.605, K.609, R.610, R.686 Ligands: ACT.13 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:F.580, B:K.609 Hydrogen bonds: B:N.502, B:N.502, B:K.609, B:R.610, B:R.610, B:R.610 Water bridges: B:G.577, B:L.578 Salt bridges: B:D.482, B:D.575 pi-Cation interactions: B:R.686

1 x PH2: 2-AMINO-6-HYDROXYMETHYL-7,8-DIHYDRO-3H-PTERIDIN-4-ONE(Non-covalent)

PH2.2: 11 residues within 4Å: Chain A: T.57, V.58, P.59, E.60, Y.61, F.163, N.165, D.208, R.326, S.328 Ligands: ATP.3 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:T.57, A:V.58, A:E.60, A:N.165, A:N.165, A:D.208, A:S.328 Water bridges: A:N.21, A:R.326 pi-Stacking: A:F.163, A:F.163 pi-Cation interactions: A:R.326

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.3: 17 residues within 4Å: Chain A: K.185, D.208, D.210, I.211, N.312, I.313, E.314, F.315, L.316, S.317, I.318, H.320, Y.322, R.326 Ligands: PH2.2, MG.4, MG.5 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:K.185, A:I.211, A:I.211, A:N.312, A:E.314, A:F.315, A:S.317 Water bridges: A:D.208, A:I.209, A:R.326, A:R.326 Salt bridges: A:K.185, A:R.326 pi-Stacking: A:F.315, A:H.320 ATP.10: 14 residues within 4Å: Chain B: L.181, K.185, D.208, D.210, I.211, N.312, I.313, E.314, F.315, L.316, S.317, H.320, Y.322 Ligands: MG.11 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:K.185, B:K.185, B:D.210, B:I.211, B:I.211, B:N.312, B:E.314, B:F.315, B:S.317, B:Y.322 Salt bridges: B:K.185

3 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: K.185, E.188, D.208 Ligands: ATP.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.188, A:E.188, A:D.208, H2O.1, H2O.6 MG.5: 3 residues within 4Å: Chain A: D.208, D.210 Ligands: ATP.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.208, A:D.208, A:D.210, H2O.1, H2O.4 MG.11: 3 residues within 4Å: Chain B: D.208, D.210 Ligands: ATP.10 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.208, B:D.208, B:D.210

1 x CA: CALCIUM ION(Non-covalent)

CA.6: 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:E.42, A:G.46, A:E.99, H2O.6

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

ACT.7: 5 residues within 4Å: Chain A: H.530, R.532, Y.544, D.550, Y.554 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.554 Water bridges: A:R.532, A:D.550 Salt bridges: A:H.530, A:R.532 ACT.8: 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:S.607, A:R.686 Salt bridges: A:R.686, A:H.688 ACT.12: 5 residues within 4Å: Chain B: H.530, R.532, Y.544, D.550, Y.554 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Y.554 Water bridges: B:R.532, B:D.550 Salt bridges: B:H.530, B:R.532 ACT.13: 5 residues within 4Å: Chain B: I.394, N.396, R.686, H.688 Ligands: CKL.9 5 PLIP interactions: 5 interactions with chain B Water bridges: B:S.607, B:R.686, B:H.688 Salt bridges: B:R.686, B:H.688 ACT.14: 3 residues within 4Å: Chain B: Y.486, N.510, E.512 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.486 Hydrogen bonds: B:N.510

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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