SMTL ID : 8ogh.1

Truncated 1-deoxy-D-xylulose 5-phosphate synthase (DXPS) from Mycobacterium tuberculosis with butylacetylphosphonate (BAP) bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x VMI: [(S)-1-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-5-[2-[oxidanyl(phosphonooxy)phosphoryl]oxyethyl]-1,3-thiazol-3-ium-2-yl]-1-oxidanyl-ethyl]-butoxy-phosphinic acid(Non-covalent)

VMI.1: 24 residues within 4Å: Chain A: H.44, P.47, T.73, H.75, R.94, Y.102, S.116, H.117, A.118, G.147, D.148, G.149, A.150, N.175, N.177, M.307, I.329, E.331, F.356, R.359, D.388, H.392 Ligands: GOL.2, MG.10 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:T.73, A:H.75, A:I.329 Hydrogen bonds: A:S.116, A:A.118, A:G.147, A:G.149, A:A.150, A:N.175, A:N.177 Water bridges: A:H.44, A:T.73, A:T.73, A:D.148, A:D.148, A:N.177, A:N.177 Salt bridges: A:H.75, A:H.75, A:K.246 pi-Stacking: A:F.356 VMI.11: 24 residues within 4Å: Chain B: G.42, H.44, P.47, T.73, H.75, R.94, Y.102, S.116, H.117, A.118, G.147, D.148, G.149, A.150, N.175, N.177, M.307, I.329, E.331, F.356, R.359, D.388, H.392 Ligands: MG.16 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:T.73, B:H.75, B:I.329 Hydrogen bonds: B:S.116, B:A.118, B:G.149, B:A.150, B:N.175, B:N.177 Water bridges: B:H.44, B:T.73, B:G.147, B:D.148, B:N.177, B:K.246, B:K.246 Salt bridges: B:H.75, B:K.246 pi-Stacking: B:F.356

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: P.310, Y.353, R.381, H.392 Ligands: VMI.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.381

10 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 5 residues within 4Å: Chain A: R.105, S.108, E.109, D.111, W.112 3 PLIP interactions: 3 interactions with chain A Water bridges: A:P.65, A:R.105, A:S.108 EDO.4: 2 residues within 4Å: Chain A: E.424, W.502 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.408 EDO.5: 4 residues within 4Å: Chain A: Y.293, R.297, G.423, D.427 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.297 EDO.6: 4 residues within 4Å: Chain A: T.416, R.417, D.445, S.447 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.417, A:R.417, A:D.445 EDO.7: 4 residues within 4Å: Chain A: A.476, F.477, R.564, L.568 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.564 Water bridges: A:A.476 EDO.8: 3 residues within 4Å: Chain A: R.542 Chain B: V.528, N.529 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:N.529 Water bridges: A:G.406, A:G.406, A:R.542, A:R.542 EDO.9: 3 residues within 4Å: Chain A: V.528, N.529 Chain B: R.542 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:N.529 Water bridges: A:N.529, B:G.406, B:G.406, B:R.542 EDO.12: 5 residues within 4Å: Chain B: R.105, S.108, E.109, D.111, W.112 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.105, B:S.108 EDO.13: 4 residues within 4Å: Chain B: Y.293, R.297, G.423, D.427 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.297, B:R.297 EDO.14: 7 residues within 4Å: Chain B: W.282, R.413, D.414, V.442, G.443, E.444, I.446 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.443, B:E.444 Water bridges: B:W.282, B:D.441

2 x MG: MAGNESIUM ION(Non-covalent)

MG.10: 3 residues within 4Å: Chain A: D.148, N.177 Ligands: VMI.1 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.148, H2O.6, H2O.9 MG.16: 3 residues within 4Å: Chain B: D.148, N.177 Ligands: VMI.11 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.148, H2O.30, H2O.34

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.15: 6 residues within 4Å: Chain B: Y.559, E.560, A.562, V.567, D.570, L.571 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.561, B:D.570 Water bridges: B:E.560, B:E.560

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gawriljuk, V.O. et al., Structure of Mycobacterium tuberculosis 1-Deoxy-D-Xylulose 5-Phosphate Synthase in Complex with Butylacetylphosphonate. Crystals (2023)

Release Date

2023-05-10

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