SMTL ID : 6ouw.1

1-deoxy-D-xylulose 5-phosphate synthase (DXPS) from Deinococcus radiodurans with enamine intermediate bound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x HTL: 2-ACETYL-THIAMINE DIPHOSPHATE(Non-covalent)

HTL.1: 20 residues within 4Å: Chain A: H.72, S.75, V.101, H.103, G.144, H.145, A.146, G.174, D.175, G.176, S.177, N.204, K.310, M.370, I.392, E.394, F.419, R.422, H.455 Ligands: MG.2 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:V.101 Hydrogen bonds: A:S.75, A:G.144, A:A.146, A:G.174, A:G.176, A:S.177, A:N.204 Water bridges: A:D.175, A:S.177, A:S.177, A:N.204 Salt bridges: A:H.103, A:K.310 pi-Stacking: A:F.419 HTL.4: 20 residues within 4Å: Chain B: H.72, S.75, V.101, H.103, G.144, H.145, A.146, G.174, D.175, G.176, S.177, N.204, K.310, M.370, I.392, E.394, F.419, R.422, H.455 Ligands: MG.5 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:V.101 Hydrogen bonds: B:S.75, B:G.144, B:A.146, B:G.174, B:G.176, B:S.177, B:N.204, B:N.204 Water bridges: B:D.175, B:S.177, B:S.177, B:N.204, B:E.394 Salt bridges: B:H.103, B:K.310 pi-Stacking: B:F.419

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.175, N.204 Ligands: HTL.1 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.175, H2O.2, H2O.2 MG.5: 3 residues within 4Å: Chain B: D.175, N.204 Ligands: HTL.4 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.175, H2O.6, H2O.7

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

NA.3: 7 residues within 4Å: Chain A: R.410, 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:H.491 NA.6: 7 residues within 4Å: Chain B: R.410, 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, P.Y. et al., X-ray crystallography-based structural elucidation of enzyme-bound intermediates along the 1-deoxy-d-xylulose 5-phosphate synthase reaction coordinate. J.Biol.Chem. (2019)

Release Date

2019-07-03

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

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

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