SMTL ID : 2o1s.2 (1 other biounit)

1-deoxy-D-xylulose 5-phosphate synthase (DXS) from Escherichia coli

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.152, N.181, K.284 Ligands: TPP.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.152, A:D.152, H2O.5 MG.4: 3 residues within 4Å: Chain B: D.152, N.181 Ligands: DPO.6 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.152, B:D.152, H2O.12

2 x K: POTASSIUM ION(Non-covalent)

K.2: 4 residues within 4Å: Chain A: P.413, G.464, Y.465, Y.467 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:G.464, A:Y.467 K.5: 6 residues within 4Å: Chain B: K.386, P.413, G.464, Y.465, Y.467, N.468 No protein-ligand interaction detected (PLIP)

1 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.3: 18 residues within 4Å: Chain A: H.80, G.121, H.122, S.123, G.151, D.152, G.153, A.154, N.181, K.284, Y.288, A.345, M.346, I.368, E.370, F.395, R.398 Ligands: MG.1 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:I.368 Hydrogen bonds: A:G.121, A:S.123, A:G.151, A:D.152, A:G.153, A:A.154, A:N.181, A:Y.288 Salt bridges: A:H.80, A:H.80, A:K.284 pi-Stacking: A:F.395

1 x DPO: DIPHOSPHATE(Non-covalent)

DPO.6: 7 residues within 4Å: Chain B: H.80, G.151, D.152, G.153, A.154, N.181 Ligands: MG.4 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.151, B:G.153, B:A.154 Water bridges: B:D.77, B:D.152, B:N.179 Salt bridges: B:H.80, B:H.80

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xiang, S. et al., Crystal Structure of 1-Deoxy-D-xylulose 5-Phosphate Synthase, a Crucial Enzyme for Isoprenoids Biosynthesis. J.Biol.Chem. (2007)

Release Date

2006-12-26

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

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

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