SMTL ID : 6jwu.1

Crystal structure of Plasmodium falciparum HPPK-DHPS wild type with STZ-DHP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

homo-dimer

Ligands

2 x XTZ: 4-{[(2-amino-4-oxo-3,4,7,8-tetrahydropteridin-6-yl)methyl]amino}-N-(1,3-thiazol-2-yl)benzenesulfonamide(Non-covalent)

XTZ.1: 19 residues within 4Å: Chain A: S.436, P.438, D.482, N.502, I.504, V.527, M.529, D.539, D.575, G.579, F.580, K.582, H.584, F.603, G.605, K.609, R.610, R.686 Ligands: PO4.3 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:F.580, A:K.609 Hydrogen bonds: A:S.436, A:N.502, A:N.502, A:G.605, A:K.609, A:R.610, A:R.610 Water bridges: A:G.577, A:K.582, A:H.584, A:G.605 Salt bridges: A:D.482, A:D.575 pi-Cation interactions: A:K.609, A:R.686 XTZ.11: 16 residues within 4Å: Chain B: D.482, N.502, I.504, 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.12 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:K.609 Hydrogen bonds: B:N.502, B:N.502, B:K.609, B:R.610 Water bridges: B:D.539, B:G.605, B:G.605, B:F.611, B:R.686 Salt bridges: B:D.482, B:D.575 pi-Stacking: B:F.580 pi-Cation interactions: B:R.610, B:R.686

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

PH2.2: 9 residues within 4Å: Chain A: T.57, V.58, E.60, Y.61, F.163, N.165, D.208, R.326, S.328 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:V.58, A:E.60, A:N.165, A:D.208, A:R.326, A:S.328 Water bridges: A:V.58 pi-Stacking: A:F.163 pi-Cation interactions: A:F.163, A:R.326

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

PO4.3: 5 residues within 4Å: Chain A: I.394, N.396, R.686, H.688 Ligands: XTZ.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.396, A:N.396 Water bridges: A:S.607, A:R.686 Salt bridges: A:R.686, A:H.688 PO4.9: 6 residues within 4Å: Chain A: Y.53, N.334, D.335, R.350, R.374, E.599 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.334, A:D.335, A:R.350, A:E.599 Water bridges: A:N.334 Salt bridges: A:R.374 PO4.10: 6 residues within 4Å: Chain A: I.49, N.50, Y.110, N.560, V.563, L.564 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:I.49, A:Y.110, A:N.560, A:N.560 Water bridges: A:N.50, A:N.50, A:R.569

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.4: 13 residues within 4Å: Chain A: L.181, 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 14 PLIP interactions: 14 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 Water bridges: A:K.185, A:K.185, A:K.185 Salt bridges: A:K.185 pi-Stacking: A:F.315, A:H.320 AMP.13: 13 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 Ligands: MG.14 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:I.211, B:I.211, B:N.312, B:E.314, B:F.315, B:S.317 Water bridges: B:K.185, B:K.185, B:K.185 pi-Stacking: B:F.315 pi-Cation interactions: B:H.320

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 3 residues within 4Å: Chain A: D.208, D.210 Ligands: AMP.4 5 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:D.208, A:D.210, H2O.2, H2O.4, AMP.4 MG.14: 3 residues within 4Å: Chain B: D.208, D.210 Ligands: AMP.13 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:D.208, B:D.208, B:D.210, B:D.210, AMP.13

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.6 CA.15: 4 residues within 4Å: Chain B: E.42, G.46, K.47, E.99 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.42, B:G.46, B:E.99, B:E.99

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

ACT.7: 4 residues within 4Å: Chain A: H.530, R.532, 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.8: 4 residues within 4Å: Chain A: K.373, R.374, L.385, E.599 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.385 Hydrogen bonds: A:R.374, A:E.599 Water bridges: A:R.374 Salt bridges: A:R.374 ACT.12: 4 residues within 4Å: Chain B: N.396, R.686, H.688 Ligands: XTZ.11 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.396 Salt bridges: B:R.686, B:H.688 ACT.16: 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 ACT.17: 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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