SMTL ID : 6jws.1

Crystal structure of Plasmodium falciparum HPPK-DHPS A437G with Pteroate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x PT1: PTEROIC ACID(Non-covalent)

PT1.1: 16 residues within 4Å: Chain A: S.436, G.437, P.438, D.482, N.502, I.504, V.527, M.529, D.575, G.579, F.580, F.603, G.605, K.609, R.610, R.686 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:K.609, A:K.609 Hydrogen bonds: A:S.436, A:N.502, A:N.502, A:G.579, A:G.605, A:K.609, A:R.610 Water bridges: A:G.577, A:F.611 Salt bridges: A:D.482, A:D.575, A:R.610 pi-Stacking: A:F.580 pi-Cation interactions: A:R.686 PT1.7: 16 residues within 4Å: Chain B: S.436, G.437, P.438, D.482, N.502, I.504, V.527, M.529, D.575, G.579, F.580, F.603, G.605, K.609, R.610, R.686 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:K.609 Hydrogen bonds: B:S.436, B:N.502, B:N.502, B:G.579, B:G.605, B:K.609, B:R.610 Water bridges: B:G.577, B:L.578, B:F.611 Salt bridges: B:D.482, B:D.575, B:R.610 pi-Stacking: B:F.580 pi-Cation interactions: B:K.609, B:R.686

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

ATP.2: 15 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, Y.322 Ligands: MG.3 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:K.185, A:K.185, A:D.210, A:I.211, A:N.312, A:E.314, A:F.315, A:S.317, A:S.317 Water bridges: A:D.208, 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.8: 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, I.318, H.320 Ligands: MG.9 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:D.208, B:D.210, B:I.211, B:N.312, B:E.314, B:F.315, B:S.317, B:S.317 Water bridges: B:H.320, B:R.326, B:R.326 Salt bridges: B:K.185, B:H.320 pi-Stacking: B:F.315, B:H.320

3 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: D.208, D.210 Ligands: ATP.2 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.3 MG.9: 3 residues within 4Å: Chain B: D.208, D.210 Ligands: ATP.8 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.208, B:D.208, B:D.210, H2O.11 MG.13: 3 residues within 4Å: Chain B: M.648, D.689, E.692 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:M.648, B:D.689, B:E.692, H2O.10, H2O.15

2 x CA: CALCIUM ION(Non-covalent)

CA.4: 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.7 CA.10: 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.18

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

ACT.5: 4 residues within 4Å: Chain A: H.530, R.532, 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.6: 3 residues within 4Å: Chain A: L.547, Q.586, K.589 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.544, A:Q.586 Salt bridges: A:K.589 ACT.11: 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:R.532 Salt bridges: B:H.530, B:R.532 ACT.12: 2 residues within 4Å: Chain B: L.547, Q.586 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Q.586 Hydrogen bonds: B:Q.586 Water bridges: B:L.547, B:L.547

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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