SMTL ID : 6ouv.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

homo-dimer

Ligands

2 x TDK: 3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-{(1S)-1-HYDROXY-1-[(R)-HYDROXY(METHOXY)PHOSPHORYL]ETHYL}-5-(2-{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-4-METHYL-1,3-THIAZOL-3-IUM(Non-covalent)

TDK.1: 28 residues within 4Å: Chain A: 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, A.369, M.370, I.392, E.394, F.419, R.422, D.451, H.455 Ligands: MG.2 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:V.101, A:F.130, A:I.208, A:A.369, A:I.392, A:I.392, A:F.419 Hydrogen bonds: A:H.72, A:S.75, 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:N.204 Water bridges: A:D.175, A:S.177, A:N.204 Salt bridges: A:H.103, A:H.103, A:K.310 pi-Stacking: A:F.419 TDK.4: 27 residues within 4Å: Chain B: 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, M.370, I.392, E.394, F.419, R.422, D.451, H.455 Ligands: MG.5 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:V.101, B:F.130, B:I.208, B:I.392, B:I.392, B:F.419 Hydrogen bonds: B:H.72, B:S.75, B:G.144, B:G.144, B:A.146, B:G.174, B:G.174, B:G.176, B:S.177, B:N.204, B:N.204 Water bridges: B:D.175, B:S.177, B:N.202, B:N.202, B:N.204 Salt bridges: B:H.103, B:H.103, B:K.310 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: TDK.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.175, A:M.206, H2O.2 MG.5: 4 residues within 4Å: Chain B: D.175, N.204, M.206 Ligands: TDK.4 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.175, B:M.206, H2O.15

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:N.437 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
B

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

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