SMTL ID : 5jaz.1

Structure of Plasmodium falciparum DXR in complex with a beta-substituted fosmidomycin analogue, LC51 and manganese

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

2 x LC5: [(2R)-2-{2-[hydroxy(methyl)amino]-2-oxoethyl}-5-(naphthalen-1-yl)pentyl]phosphonic acid(Non-covalent)

LC5.1: 21 residues within 4Å: Chain A: K.139, D.165, S.166, E.167, S.203, S.204, G.205, G.206, M.232, I.236, S.240, N.245, K.246, E.249, C.272, H.275, P.292, D.293, M.294 Ligands: MN.2, GOL.3 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:K.139, A:S.166, A:S.204, A:S.204, A:G.205, A:G.206, A:S.240, A:N.245, A:K.246 Water bridges: A:S.203, A:K.246 Salt bridges: A:D.165, A:E.167, A:E.249 pi-Stacking: A:P.292 LC5.6: 22 residues within 4Å: Chain B: K.139, D.165, S.166, E.167, S.203, S.204, G.205, G.206, W.230, M.232, I.236, S.240, N.245, K.246, E.249, C.272, H.275, P.292, D.293, M.294 Ligands: MN.7, GOL.8 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:W.230, B:P.292 Hydrogen bonds: B:K.139, B:S.166, B:S.204, B:S.204, B:G.205, B:G.206, B:S.240, B:N.245, B:K.246 Water bridges: B:K.246 Salt bridges: B:D.165, B:E.167, B:E.249

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 6 residues within 4Å: Chain A: K.139, D.165, S.166, E.167, E.249 Ligands: LC5.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.165, A:E.167, A:E.167, A:E.249 MN.7: 6 residues within 4Å: Chain B: K.139, D.165, S.166, E.167, E.249 Ligands: LC5.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.165, B:E.167, B:E.167, B:E.249

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 10 residues within 4Å: Chain A: S.166, E.167, C.202, S.203, S.204, H.269, C.272, I.274, H.275 Ligands: LC5.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.166, A:S.203, A:I.274, A:H.275 GOL.4: 5 residues within 4Å: Chain A: Y.47, N.49, H.70, I.115, Q.119 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.47 GOL.8: 10 residues within 4Å: Chain B: S.166, E.167, C.202, S.203, S.204, H.269, C.272, I.274, H.275 Ligands: LC5.6 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.166, B:S.203, B:I.274 GOL.9: 6 residues within 4Å: Chain B: K.157, K.160, L.181, T.183, K.184, Q.187 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.160, B:L.181, B:Q.187, B:Q.187 Water bridges: B:K.184, B:K.184 GOL.10: 6 residues within 4Å: Chain B: G.18, Y.47, V.48, N.49, H.70, I.115 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.18, B:Y.47 Water bridges: B:N.49

3 x FMT: FORMIC ACID(Non-functional Binders)

FMT.5: 6 residues within 4Å: Chain A: Q.173, C.174, L.175 Chain B: Q.173, C.174, L.175 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.173 FMT.11: 6 residues within 4Å: Chain B: S.191, I.196, N.197, V.259, D.260, D.263 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.191, B:I.196, B:D.260 FMT.12: 5 residues within 4Å: Chain B: V.143, N.347, F.348, P.350, T.351 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.147, B:T.351

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sooriyaarachchi, S. et al., Targeting an Aromatic Hotspot in Plasmodium falciparum 1-Deoxy-d-xylulose-5-phosphate Reductoisomerase with beta-Arylpropyl Analogues of Fosmidomycin. Chemmedchem (2016)

Release Date

2016-08-24

Peptides

1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic

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