SMTL ID : 8zxx.1

PfDXR - Mn2+ - NADPH - TAKK442 quaternary complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.23 Å

Oligo State

homo-dimer

Ligands

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

NDP.1: 28 residues within 4Å: Chain A: G.10, S.11, T.12, G.13, S.14, I.15, Y.39, V.40, N.41, K.42, S.43, H.62, G.106, I.107, D.108, S.109, Q.111, A.129, N.130, K.131, E.132, D.157, W.222, M.224, G.225, I.228, M.286 Ligands: 01.3 32 PLIP interactions: 32 interactions with chain A Hydrophobic interactions: A:I.15, A:I.228 Hydrogen bonds: A:G.10, A:T.12, A:T.12, A:T.12, A:G.13, A:S.14, A:S.14, A:S.14, A:I.15, A:N.41, A:K.42, A:S.43, A:S.43, A:H.62, A:I.107, A:D.108, A:S.109, A:Q.111, A:N.130, A:K.131, A:G.225 Water bridges: A:N.41, A:N.41, A:E.132, A:E.132, A:E.132, A:E.132, A:K.226, A:K.227 pi-Stacking: A:Y.39 NDP.5: 28 residues within 4Å: Chain B: G.10, S.11, T.12, G.13, S.14, I.15, Y.39, V.40, N.41, K.42, S.43, H.62, G.106, I.107, D.108, S.109, Q.111, A.129, N.130, K.131, E.132, D.157, W.222, M.224, G.225, I.228, M.286 Ligands: 01.7 35 PLIP interactions: 35 interactions with chain B Hydrophobic interactions: B:I.15, B:I.228 Hydrogen bonds: B:G.10, B:T.12, B:T.12, B:T.12, B:G.13, B:S.14, B:S.14, B:S.14, B:I.15, B:N.41, B:K.42, B:S.43, B:S.43, B:H.62, B:I.107, B:D.108, B:D.108, B:S.109, B:Q.111, B:N.130, B:K.131, B:G.225 Water bridges: B:Y.39, B:Y.39, B:N.41, B:N.41, B:E.132, B:E.132, B:E.132, B:E.132, B:K.226, B:K.227 pi-Stacking: B:Y.39

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

MN.2: 6 residues within 4Å: Chain A: K.131, D.157, S.158, E.159, E.241 Ligands: 01.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.157, A:E.159, A:E.159, A:E.241 MN.6: 6 residues within 4Å: Chain B: K.131, D.157, S.158, E.159, E.241 Ligands: 01.7 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.157, B:E.159, B:E.159, B:E.241

2 x 01: [(~{S})-(4-hexoxyphenyl)-[2-[methyl(oxidanyl)amino]-2-oxidanylidene-ethyl]sulfanyl-methyl]phosphonic acid

01.3: 22 residues within 4Å: Chain A: K.131, D.157, S.158, E.159, S.195, S.196, K.221, W.222, M.224, I.228, S.232, N.237, K.238, E.241, K.262, E.263, C.264, P.284, M.286 Ligands: NDP.1, MN.2, GOL.4 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:K.221, A:P.284 Hydrogen bonds: A:K.131, A:S.158, A:E.159, A:S.196, A:G.198, A:S.232, A:N.237, A:K.238 Water bridges: A:S.195, A:S.195, A:G.197, A:G.197 Salt bridges: A:D.157, A:E.159, A:E.241 01.7: 22 residues within 4Å: Chain B: K.131, D.157, S.158, E.159, S.195, S.196, K.221, W.222, M.224, I.228, S.232, N.237, K.238, E.241, K.262, E.263, C.264, P.284, M.286 Ligands: NDP.5, MN.6, GOL.8 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:K.221, B:P.284 Hydrogen bonds: B:K.131, B:S.158, B:E.159, B:S.196, B:G.198, B:S.232, B:N.237, B:K.238 Water bridges: B:S.195, B:S.195, B:G.197, B:G.197 Salt bridges: B:D.157, B:E.159, B:E.241

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 10 residues within 4Å: Chain A: S.158, E.159, C.194, S.195, S.196, H.261, C.264, I.266, H.267 Ligands: 01.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.195, A:I.266 Water bridges: A:S.158, A:S.196 GOL.8: 10 residues within 4Å: Chain B: S.158, E.159, C.194, S.195, S.196, H.261, C.264, I.266, H.267 Ligands: 01.7 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.195, B:I.266, B:H.267 Water bridges: B:S.158, B:S.196

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Knak, T. et al., Expanding the Chemical Space of Reverse Fosmidomycin Analogs. Acs Med.Chem.Lett. (2025)

Release Date

2025-05-21

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

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