SMTL ID : 9job.1

PfDXR - Mn2+ - NADPH - MAMK89 quaternary complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.39 Å

Oligo State

homo-dimer

Ligands

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

NDP.1: 26 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, Q.185, A.203, N.204, K.205, E.206, D.231, W.296, M.298, I.302, M.360 Ligands: UW0.3 22 PLIP interactions: 22 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:Q.185, A:E.206 Water bridges: A:G.90, A:Y.113, A:Y.113 pi-Stacking: A:Y.113 NDP.4: 25 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, Q.185, A.203, N.204, K.205, E.206, D.231, W.296, I.302, M.360 Ligands: UW0.6 32 PLIP interactions: 32 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:Q.185, B:N.204, B:K.205 Water bridges: B:T.86, B:S.117, B:D.182, B:D.182, B:E.206, B:E.206, B:E.206, B:G.299, B:G.299 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: UW0.3 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: UW0.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.231, B:E.233, B:E.233, B:E.315

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

UW0.3: 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: NDP.1, MN.2 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:K.295, A:W.296, A:W.296, A:I.302, A:P.358 Hydrogen bonds: A:K.205, A:S.232, A:S.270, A:G.272, A:S.306, A:N.311, A:K.312, A:K.312 Water bridges: A:S.269, A:S.269, A:G.271, A:G.271 pi-Stacking: A:H.341 UW0.6: 20 residues within 4Å: Chain B: K.205, D.231, S.232, E.233, S.269, S.270, 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: NDP.4, MN.5 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:W.296, B:W.296, B:I.302, B:P.358 Hydrogen bonds: B:K.205, B:S.232, B:S.270, B:S.270, B:S.306, B:N.311, B:K.312 Water bridges: B:S.269, B:G.271, B:G.271, B:N.311 pi-Stacking: B:H.341

3 x CA: CALCIUM ION(Non-covalent)

CA.7: 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.4, H2O.20 CA.8: 2 residues within 4Å: Chain B: S.139, E.143 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:S.139, B:E.143, B:E.143 CA.9: 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.16, H2O.17, H2O.18, H2O.24

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

Related Entries With Identical Sequence