SMTL ID : 8bzx.1

1-deoxy-D-xylulose 5-phosphate synthase from Klebsiella pneumoniae (kpDXPS),co-crystal with thiamine monophosphate analog

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

2 x SW6: 2-[4-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-3-methyl-5-propanoyl-thiophen-2-yl]ethyl dihydrogen phosphate(Non-covalent)

SW6.1: 24 residues within 4Å: Chain A: H.49, V.78, H.80, F.107, G.121, H.122, S.123, G.151, D.152, G.153, A.154, M.183, S.184, I.185, P.310, A.311, M.312, I.334, E.336, F.361, R.364, D.393, H.397 Ligands: MG.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.78, A:F.107, A:F.361 Hydrogen bonds: A:S.123, A:G.151, A:G.151, A:G.153, A:A.154, A:H.397 Water bridges: A:K.250 Salt bridges: A:H.80 pi-Stacking: A:F.361 SW6.3: 26 residues within 4Å: Chain B: H.49, V.78, H.80, F.107, G.121, H.122, S.123, G.151, D.152, G.153, A.154, N.181, M.183, S.184, I.185, H.265, P.310, A.311, M.312, I.334, E.336, F.361, R.364, D.393, H.397 Ligands: MG.4 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:V.78, B:H.80, B:F.107, B:A.311, B:I.334, B:I.334, B:F.361 Hydrogen bonds: B:S.123, B:G.153, B:A.154 Water bridges: B:G.151, B:G.151, B:N.181 Salt bridges: B:H.80 pi-Stacking: B:F.361

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.152, N.181, M.183, S.184 Ligands: SW6.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.152, A:M.183 MG.4: 5 residues within 4Å: Chain B: D.152, N.181, M.183, S.184 Ligands: SW6.3 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.152, B:M.183 MG.5: 1 residues within 4Å: Chain B: N.215 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chan, A.H.Y. et al., Design of thiamine analogues for inhibition of thiamine diphosphate (ThDP)-dependent enzymes: Systematic investigation through Scaffold-Hopping and C2-Functionalisation. Bioorg.Chem. (2023)

Release Date

2023-06-14

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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