SMTL ID : 6xxg.1

Structure of truncated 1-deoxy-D-xylulose 5-phosphate synthase (DXS) from Deinococcus radiodurans

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

5 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.156, G.157, N.185, E.186 Ligands: TPP.3 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.156, H2O.1, H2O.5 MG.5: 4 residues within 4Å: Chain A: E.558, F.559, Q.560, E.561 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:F.559, A:E.561, H2O.6, H2O.6, H2O.9 MG.6: 5 residues within 4Å: Chain B: D.156, G.157, N.185, E.186 Ligands: TPP.10 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.156, H2O.11, H2O.14 MG.8: 4 residues within 4Å: Chain B: E.558, F.559, Q.560, E.561 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:F.559, B:E.561, H2O.14, H2O.15, H2O.18 MG.9: 2 residues within 4Å: Chain B: G.8, D.11 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:G.8, B:D.11, H2O.16

6 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: Q.85, V.153, G.155, N.183 No protein-ligand interaction detected (PLIP) CA.4: 7 residues within 4Å: Chain A: R.354, N.381, A.432, H.435, D.436, G.437, F.439 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:A.432, A:H.435, A:G.437, H2O.5, H2O.7 CA.7: 6 residues within 4Å: Chain B: K.420, E.424, E.465, L.467, N.499, R.501 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.424, B:E.465 CA.11: 7 residues within 4Å: Chain B: R.354, N.381, A.432, H.435, D.436, G.437, F.439 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:A.432, B:H.435, B:G.437, H2O.14, H2O.17 CA.12: 7 residues within 4Å: Chain A: H.126, T.129, R.366 Chain B: D.369, Q.370, H.373, D.374 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.369, B:D.374 CA.13: 2 residues within 4Å: Chain B: G.516, R.517 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:G.516, H2O.17

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.3: 19 residues within 4Å: Chain A: S.56, V.82, H.84, G.125, H.126, A.127, G.155, D.156, G.157, S.158, N.185, A.313, M.314, I.336, E.338, F.363, R.366, H.399 Ligands: MG.1 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:H.126, A:F.363 Hydrogen bonds: A:S.56, A:G.125, A:A.127, A:G.155, A:G.157, A:S.158, A:N.185 Water bridges: A:D.81, A:D.156, A:N.185, A:E.338 Salt bridges: A:H.84 pi-Stacking: A:F.363 TPP.10: 20 residues within 4Å: Chain B: S.56, V.82, H.84, G.125, H.126, A.127, G.155, D.156, G.157, S.158, N.185, K.254, A.313, M.314, I.336, E.338, F.363, R.366, H.399 Ligands: MG.6 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:I.336, B:F.363 Hydrogen bonds: B:S.56, B:G.125, B:A.127, B:G.155, B:G.157, B:S.158, B:N.185 Water bridges: B:G.155, B:D.156, B:N.183, B:N.183, B:N.185, B:R.366 Salt bridges: B:H.84 pi-Stacking: B:F.363

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gierse, R.M. et al., Identification of a 1-deoxy-D-xylulose-5-phosphate synthase (DXS) mutant with improved crystallographic properties. Biochem.Biophys.Res.Commun. (2021)

Release Date

2021-01-20

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