SMTL ID : 3wqq.1

Crystal structure of PfDXR complexed with inhibitor-3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-dimer

Ligands

2 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.1: 27 residues within 4Å: Chain A: G.84, S.85, T.86, G.87, S.88, I.89, Y.113, V.114, N.115, K.116, S.117, H.136, G.180, I.181, D.182, S.183, Q.185, A.203, N.204, K.205, E.206, D.231, M.298, G.299, I.302, M.360 Ligands: IB3.3 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:I.89, A:I.302 Hydrogen bonds: A:G.84, A:T.86, A:T.86, A:T.86, A:S.88, A:S.88, A:S.88, A:I.89, A:N.115, A:K.116, A:S.117, A:S.117, A:H.136, A:I.181, A:D.182, A:D.182, A:S.183, A:Q.185, A:N.204, A:E.206, A:G.299 Water bridges: A:G.87, A:N.115 pi-Stacking: A:Y.113 NDP.4: 27 residues within 4Å: Chain B: G.84, T.86, G.87, S.88, I.89, Y.113, V.114, N.115, K.116, S.117, H.136, G.180, I.181, D.182, S.183, Q.185, A.203, N.204, K.205, E.206, D.231, W.296, M.298, G.299, I.302, M.360 Ligands: IB3.8 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:I.89, B:I.302 Hydrogen bonds: B:G.84, B:T.86, B:T.86, B:T.86, B:G.87, B:S.88, B:S.88, B:S.88, B:I.89, B:N.115, B:K.116, B:S.117, B:S.117, B:H.136, B:I.181, B:D.182, B:S.183, B:N.204, B:G.299 Water bridges: B:D.182, B:K.301 pi-Stacking: B:Y.113

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: K.205, D.231, S.232, E.233, E.315 Ligands: IB3.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.231, A:E.233, A:E.233, A:E.315 MG.5: 5 residues within 4Å: Chain B: K.205, D.231, E.233, E.315 Ligands: IB3.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.231, B:E.233, B:E.233, B:E.315

2 x IB3: [(1S)-4-[hydroxy(methyl)amino]-1-(4-methylphenyl)-4-oxobutyl]phosphonic acid(Non-covalent)

IB3.3: 19 residues within 4Å: Chain A: K.205, D.231, S.232, E.233, S.269, S.270, K.295, W.296, M.298, I.302, S.306, N.311, K.312, E.315, C.338, P.358, M.360 Ligands: NDP.1, MG.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:I.302, A:P.358 Hydrogen bonds: A:K.205, A:S.232, A:E.233, A:S.269, A:S.270, A:N.311, A:K.312 Water bridges: A:S.269, A:G.271, A:G.271, A:K.312 IB3.8: 18 residues within 4Å: Chain B: K.205, D.231, S.232, E.233, S.269, S.270, K.295, W.296, M.298, I.302, S.306, N.311, K.312, E.315, C.338, P.358 Ligands: NDP.4, MG.5 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:K.295, B:W.296, B:I.302, B:P.358 Hydrogen bonds: B:K.205, B:S.232, B:S.269, B:S.270, B:N.311, B:K.312 Water bridges: B:S.269, B:G.271, B:S.306, B:K.312

2 x CA: CALCIUM ION(Non-covalent)

CA.6: 3 residues within 4Å: Chain A: D.242 Chain B: Q.239, L.241 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:Q.239, A:D.242, H2O.1, H2O.5, H2O.6 CA.7: 1 residues within 4Å: Chain B: N.452 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Konzuch, S. et al., Binding Modes of Reverse Fosmidomycin Analogs toward the Antimalarial Target IspC. J.Med.Chem. (2014)

Release Date

2014-11-26

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

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

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