SMTL ID : 8v9i.1

1-deoxy-D-xylulose 5-phosphate synthase (DXPS) from Deinococcus radiodurans with D-phenylalanine-derived triazole acetylphosphonate (D-PheTrAP) bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

homo-dimer

Ligands

2 x 01: 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-2-{(1S)-1-[(S)-(2-{1-[(1R)-1-carboxy-2-phenylethyl]-1H-1,2,3-triazol-4-yl}ethoxy)(hydroxy)phosphoryl]-1-hydroxyethyl}-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium

01.1: 34 residues within 4Å: Chain A: G.70, L.71, H.72, S.75, V.101, H.103, F.130, G.144, H.145, A.146, G.174, D.175, G.176, S.177, N.202, N.204, M.206, S.207, I.208, K.310, H.325, G.326, M.370, I.392, E.394, Y.416, F.419, R.422, R.444, D.451, H.455, R.501 Ligands: MG.2, BGQ.4 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:V.101, A:F.130, A:I.208, A:I.208, A:I.392, A:I.392, A:Y.416, A:F.419 Hydrogen bonds: A:G.144, A:G.144, A:A.146, A:G.174, A:G.174, A:G.176, A:S.177, A:N.202, A:N.204, A:H.325, A:Y.416, A:R.444 Water bridges: A:D.175, A:S.177, A:N.204 Salt bridges: A:H.103, A:H.103, A:K.310, A:R.444, A:R.501 pi-Stacking: A:F.419 01.5: 33 residues within 4Å: Chain B: G.70, L.71, H.72, S.75, V.101, H.103, F.130, G.144, H.145, A.146, G.174, D.175, G.176, S.177, N.202, N.204, M.206, S.207, I.208, K.310, H.325, G.326, M.370, I.392, E.394, Y.416, F.419, R.422, R.444, D.451, H.455, R.501 Ligands: MG.6 28 PLIP interactions: 28 interactions with chain B Hydrophobic interactions: B:V.101, B:F.130, B:I.208, B:I.208, B:I.392, B:I.392, B:Y.416, B:F.419 Hydrogen bonds: B:G.144, B:G.144, B:A.146, B:G.174, B:G.174, B:G.176, B:S.177, B:N.202, B:N.204, B:H.325, B:R.444 Water bridges: B:D.175, B:S.177, B:N.204 Salt bridges: B:H.103, B:H.103, B:K.310, B:R.444, B:R.501 pi-Stacking: B:F.419

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.175, N.204, M.206 Ligands: 01.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.175, A:M.206, H2O.2 MG.6: 4 residues within 4Å: Chain B: D.175, N.204, M.206 Ligands: 01.5 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.175, B:M.206, H2O.14

2 x NA: SODIUM ION(Non-functional Binders)

NA.3: 6 residues within 4Å: Chain A: N.437, A.488, H.491, D.492, G.493, F.495 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.410, A:A.488 NA.7: 6 residues within 4Å: Chain B: N.437, A.488, H.491, D.492, G.493, F.495 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.410, B:A.488

1 x BGQ: 2-HYDROXY BUTANE-1,4-DIOL(Non-covalent)

BGQ.4: 7 residues within 4Å: Chain A: I.208, I.322, H.325, M.370, E.372, G.373 Ligands: 01.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.322

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Coco, L.B. et al., Potent Inhibition of E. coli DXP Synthase by a gem -Diaryl Bisubstrate Analog. Acs Infect Dis. (2024)

Release Date

2024-04-24

Peptides

1-deoxy-D-xylulose-5-phosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

1-deoxy-D-xylulose-5-phosphate synthase

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