SMTL ID : 7a9h.1

Truncated 1-deoxy-D-xylulose 5-phosphate synthase (DXS) from Mycobacterium tuberculosis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.172, G.173, N.201 Ligands: TPP.2 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.172, H2O.3, H2O.7 MG.3: 4 residues within 4Å: Chain B: D.172, G.173, N.201 Ligands: TPP.4 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.172, H2O.15, H2O.20

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.2: 21 residues within 4Å: Chain A: P.71, T.97, H.99, S.140, H.141, A.142, G.171, D.172, G.173, A.174, N.199, N.201, K.270, A.329, A.330, M.331, I.353, E.355, F.380, R.383 Ligands: MG.1 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:A.330, A:F.380, A:F.380 Hydrogen bonds: A:S.140, A:A.142, A:G.173, A:A.174, A:N.199, A:N.201 Water bridges: A:D.96, A:T.97, A:D.172, A:N.201, A:N.201, A:K.270, A:K.270, A:K.270 Salt bridges: A:H.99 TPP.4: 21 residues within 4Å: Chain B: P.71, T.97, H.99, S.140, H.141, A.142, G.171, D.172, G.173, A.174, N.199, N.201, K.270, A.329, A.330, M.331, I.353, E.355, F.380, R.383 Ligands: MG.3 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:A.330, B:I.353, B:F.380 Hydrogen bonds: B:S.140, B:A.142, B:G.173, B:A.174, B:N.199, B:N.201 Water bridges: B:T.97, B:T.97, B:G.171, B:D.172, B:N.201, B:K.270 Salt bridges: B:H.99 pi-Stacking: B:F.380

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gierse, R.M. et al., First crystal structures of 1-deoxy-D-xylulose 5-phosphate synthase (DXPS) from Mycobacterium tuberculosis indicate a distinct mechanism of intermediate stabilization. Sci Rep (2022)

Release Date

2022-03-23

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

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