SMTL ID : 6kcm.1

Crystal structure of Plasmodium falciparum HPPK-DHPS S436F/A437G/A613S with pterin and p-hydrobenzoate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x PE0: PTERINE(Non-covalent)

PE0.1: 12 residues within 4Å: Chain A: D.482, N.502, I.504, M.529, D.575, F.580, F.603, G.605, K.609, R.686 Ligands: PHB.2, GOL.4 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.502, A:N.502, A:G.605, A:K.609 Water bridges: A:R.686 Salt bridges: A:D.482, A:D.575 pi-Stacking: A:F.580 pi-Cation interactions: A:R.686 PE0.8: 12 residues within 4Å: Chain B: D.482, N.502, I.504, M.529, D.575, F.580, F.603, G.605, K.609, R.686 Ligands: PHB.9, GOL.11 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:N.502, B:N.502, B:K.609, B:R.686 Water bridges: B:L.578, B:G.605 Salt bridges: B:D.575 pi-Stacking: B:F.580 pi-Cation interactions: B:R.686

2 x PHB: P-HYDROXYBENZOIC ACID(Non-covalent)

PHB.2: 6 residues within 4Å: Chain A: G.579, F.580, K.609, R.610 Ligands: PE0.1, GOL.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.580, A:K.609 Hydrogen bonds: A:G.579, A:R.610 Water bridges: A:F.611 Salt bridges: A:R.610 PHB.9: 6 residues within 4Å: Chain B: M.538, G.579, F.580, K.609, R.610 Ligands: PE0.8 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.580, B:K.609, B:K.609 Hydrogen bonds: B:G.579, B:R.610 Water bridges: B:F.611 Salt bridges: B:R.610 pi-Cation interactions: B:K.609

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

ATP.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.5 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:D.208, A:I.211, A:N.312, A:E.314, A:F.315, A:S.317, A:S.317 Water bridges: A:K.185, A:K.185, A:H.320, A:H.320, A:R.326, A:R.326 Salt bridges: A:K.185, A:H.320 pi-Stacking: A:F.315, A:H.320 ATP.10: 15 residues within 4Å: Chain B: L.181, K.185, R.205, D.208, D.210, I.211, N.312, I.313, E.314, F.315, L.316, S.317, I.318, H.320 Ligands: MG.12 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:D.210, B:I.211, B:E.314, B:F.315, B:S.317, B:S.317 Water bridges: B:K.185 Salt bridges: B:K.185, B:R.205, B:H.320 pi-Stacking: B:F.315, B:H.320

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: N.396, S.607, R.608, R.686, H.688 Ligands: PE0.1, PHB.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.396, A:R.608, A:R.686, A:R.686 GOL.11: 5 residues within 4Å: Chain B: I.394, N.396, R.686, H.688 Ligands: PE0.8 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.396, B:R.686, B:R.686, B:H.688 Water bridges: B:S.607, B:H.688

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 3 residues within 4Å: Chain A: D.208, D.210 Ligands: ATP.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.208, A:D.208, A:D.210, H2O.3 MG.12: 3 residues within 4Å: Chain B: D.208, D.210 Ligands: ATP.10 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.208, B:D.208, B:D.210, H2O.8

2 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.3 CA.13: 3 residues within 4Å: Chain B: E.42, G.46, 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.10

2 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 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.554 Salt bridges: A:H.530, A:R.532 ACT.14: 5 residues within 4Å: Chain B: H.530, R.532, Y.544, D.550, Y.554 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.554 Water bridges: B:R.532 Salt bridges: B:H.530, B:R.532

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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