SMTL ID : 9joa.1

PfDXR - Mn2+ - MAMK89 ternary complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 6 residues within 4Å: Chain A: K.205, D.231, S.232, E.233, E.315 Ligands: UW0.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.231, A:E.233, A:E.233, A:E.315 MN.4: 6 residues within 4Å: Chain B: K.205, D.231, S.232, E.233, E.315 Ligands: UW0.5 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.231, B:E.233, B:E.233, B:E.315

2 x UW0: [(1~{S})-4-oxidanylidene-4-[oxidanyl(3-phenylpropyl)amino]-1-phenyl-butyl]phosphonic acid(Non-covalent)

UW0.2: 21 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, H.341, P.358, D.359, M.360 Ligands: MN.1, GOL.3 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:K.295, A:W.296, A:I.302, A:P.358 Hydrogen bonds: A:K.205, A:S.232, A:S.270, A:S.306, A:N.311, A:K.312, A:K.312 Water bridges: A:S.269, A:S.269, A:G.271, A:N.311 pi-Stacking: A:H.341 UW0.5: 21 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, H.341, P.358, D.359, M.360 Ligands: MN.4, GOL.9 16 PLIP interactions: 16 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.270, B:S.270, B:G.272, B:N.311, B:K.312 Water bridges: B:S.269, B:G.271, B:G.271, B:K.312 pi-Stacking: B:H.341

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 10 residues within 4Å: Chain A: S.232, E.233, C.268, S.269, S.270, H.335, C.338, I.340, H.341 Ligands: UW0.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.232, A:S.269, A:I.340 GOL.9: 10 residues within 4Å: Chain B: S.232, E.233, C.268, S.269, S.270, H.335, C.338, I.340, H.341 Ligands: UW0.5 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.232, B:S.269, B:I.340, B:H.341

3 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: 2 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:Q.239, B:L.241, A:D.242, H2O.14, H2O.20 CA.7: 2 residues within 4Å: Chain B: S.139, E.143 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.139, B:E.143, B:E.143, H2O.20 CA.8: 1 residues within 4Å: Chain B: D.329 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.329, H2O.17, H2O.18, H2O.22, H2O.23

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abdullaziz, M.A. et al., Reverse N-Substituted Hydroxamic Acid Derivatives of Fosmidomycin Target a Previously Unknown Subpocket of 1-Deoxy-d-xylulose 5-Phosphate Reductoisomerase (DXR). ACS Infect Dis (2024)

Release Date

2025-01-01

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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