SMTL ID : 9kp9.1

PfDXR - Mn2+ - NADPH - TAKK443 quaternary complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.13 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.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, W.296, M.298, G.299, I.302, M.360 Ligands: 01.3 34 PLIP interactions: 34 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:G.87, 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:S.183, A:Q.185, A:N.204, A:K.205, A:G.299 Water bridges: A:G.90, A:N.115, A:E.206, A:E.206, A:E.206, A:E.206, A:K.300, A:K.300, A:K.300, A:K.301 pi-Stacking: A:Y.113 NDP.4: 28 residues within 4Å: Chain B: 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, W.296, M.298, G.299, I.302, M.360 Ligands: 01.6 35 PLIP interactions: 35 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:D.182, B:S.183, B:Q.185, B:N.204, B:K.205, B:G.299 Water bridges: B:G.90, B:N.115, B:E.206, B:E.206, B:E.206, B:E.206, B:K.300, B:K.300, B:K.300, B:K.301 pi-Stacking: B:Y.113

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

MN.2: 6 residues within 4Å: Chain A: K.205, D.231, S.232, E.233, E.315 Ligands: 01.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.231, A:E.233, A:E.233, A:E.315 MN.5: 6 residues within 4Å: Chain B: K.205, D.231, S.232, E.233, E.315 Ligands: 01.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.231, B:E.233, B:E.233, B:E.315

2 x 01: [(~{S})-(3-hexoxyphenyl)-[2-[methyl(oxidanyl)amino]-2-oxidanylidene-ethyl]sulfanyl-methyl]phosphonic acid

01.3: 21 residues within 4Å: Chain A: K.205, D.231, S.232, E.233, S.269, S.270, H.293, P.294, 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, MN.2 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:P.294, A:P.358 Hydrogen bonds: A:K.205, A:S.232, A:S.270, A:S.270, A:G.272, A:N.311, A:K.312, A:K.312 Water bridges: A:S.269, A:S.270, A:G.271, A:G.271, A:K.312 Salt bridges: A:D.231, A:E.233, A:E.315 01.6: 21 residues within 4Å: Chain B: K.205, D.231, S.232, E.233, S.269, S.270, H.293, P.294, K.295, W.296, M.298, I.302, S.306, N.311, K.312, E.315, C.338, P.358, M.360 Ligands: NDP.4, MN.5 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:P.294, 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, B:K.312 Water bridges: B:S.269, B:S.270, B:G.271, B:G.271, B:K.312 Salt bridges: B:D.231, B:E.233, B:E.315

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

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