SMTL ID : 7a9g.1

Truncated 1-deoxy-D-xylulose 5-phosphate synthase (DXS) from Mycobacterium tuberculosis with intermediate 2-acetyl-thiamine diphosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

HTL.1: 23 residues within 4Å: Chain A: H.68, P.71, T.97, H.99, Y.126, S.140, H.141, A.142, G.171, D.172, G.173, A.174, N.199, N.201, K.308, E.321, A.368, M.369, I.391, E.393, F.418, R.421 Ligands: MG.2 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:H.99, A:I.391, A:F.418 Hydrogen bonds: A:S.140, A:A.142, A:G.173, A:A.174, A:N.199, A:N.201 Water bridges: A:D.96, A:G.171, A:D.172, A:N.201, A:K.308, A:K.308, A:H.454 Salt bridges: A:H.99, A:K.308 HTL.13: 22 residues within 4Å: Chain B: H.68, P.71, T.97, H.99, Y.126, S.140, H.141, A.142, G.171, D.172, G.173, A.174, N.199, N.201, K.308, A.368, M.369, I.391, E.393, F.418, R.421 Ligands: MG.14 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:H.99, B:I.391 Hydrogen bonds: B:S.140, B:A.142, B:G.171, B:G.173, B:A.174, B:N.199, B:N.201 Water bridges: B:T.97, B:T.97, B:D.172, B:D.172, B:N.201, B:K.308, B:K.308 Salt bridges: B:H.99, B:K.308 pi-Stacking: B:F.418

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.172, G.173, N.201, K.308 Ligands: HTL.1 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.172, H2O.3, H2O.7 MG.14: 5 residues within 4Å: Chain B: D.172, G.173, N.201, K.308 Ligands: HTL.13 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.172, H2O.11, H2O.14

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

PEG.3: 10 residues within 4Å: Chain A: A.404, M.405, G.407, H.433, K.434, L.435, P.436, D.491, D.492 Chain B: R.129 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.129 PEG.4: 8 residues within 4Å: Chain A: M.369, P.372, Y.415, R.443, T.447, D.450, H.454, K.501 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.443, A:R.443, A:H.454 PEG.5: 6 residues within 4Å: Chain A: R.48, R.55, E.77, H.281, M.310, G.311 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.48, A:R.48 Water bridges: A:R.55, A:E.77 PEG.6: 9 residues within 4Å: Chain A: K.120, G.121, Y.621, E.622, H.623, A.624, V.629, D.632, L.633 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.632 Water bridges: A:G.121, A:E.622, A:H.623 PEG.8: 5 residues within 4Å: Chain A: Q.32, I.33, R.34, D.38, L.42 No protein-ligand interaction detected (PLIP) PEG.17: 7 residues within 4Å: Chain B: R.110, D.113, T.116, G.121, G.122, L.123, E.131 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.122 PEG.19: 10 residues within 4Å: Chain A: F.620 Chain B: A.431, L.432, K.434, P.467, G.468, R.470, D.492, G.493, P.494 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.434, B:D.492 PEG.20: 5 residues within 4Å: Chain B: R.55, E.77, H.281, M.310, G.311 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.55, B:R.55 PEG.23: 9 residues within 4Å: Chain B: K.120, G.121, Y.621, E.622, H.623, A.624, V.629, D.632, L.633 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.632 Water bridges: B:G.121, B:E.622, B:H.623

6 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.7: 6 residues within 4Å: Chain A: R.470, E.486, A.487, V.490, W.564, P.567 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.470 PGE.9: 5 residues within 4Å: Chain A: L.527, H.551, N.552, Q.553, G.554 No protein-ligand interaction detected (PLIP) PGE.10: 12 residues within 4Å: Chain A: V.590, D.613, V.614, G.615, P.617, L.633, G.634, L.635, D.639, V.640, R.643 Chain B: R.604 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.615, A:R.643 Water bridges: A:D.639, A:R.643 PGE.16: 7 residues within 4Å: Chain B: L.511, L.520, A.521, L.544, A.547, K.548, H.551 No protein-ligand interaction detected (PLIP) PGE.21: 6 residues within 4Å: Chain B: R.470, E.486, D.489, V.490, W.564, P.567 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.470, B:R.470 PGE.22: 7 residues within 4Å: Chain A: T.159, H.161 Chain B: R.360, D.361, G.406, G.407, L.408 No protein-ligand interaction detected (PLIP)

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.11: 8 residues within 4Å: Chain A: R.110, D.113, T.116, G.121, G.122, L.123, A.130, E.131 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.130 Water bridges: A:S.124 PG4.18: 12 residues within 4Å: Chain A: R.604 Chain B: V.590, D.613, V.614, G.615, P.617, L.633, G.634, L.635, D.639, V.640, R.643 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Water bridges: A:R.604 Hydrogen bonds: B:G.615, B:R.643

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 10 residues within 4Å: Chain A: A.431, L.432, K.434, P.467, G.468, R.470, D.492, G.493, P.494 Chain B: F.620 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.431, A:K.434, A:D.492

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.15: 6 residues within 4Å: Chain B: M.369, P.372, Y.415, R.443, H.454, K.501 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.415 Salt bridges: B:R.443, B:H.454, B:K.501

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gierse, R.M. et al., First crystal structures of 1-deoxy-D-xylulose 5-phosphate synthase (DXPS) from Mycobacterium tuberculosis indicate a distinct mechanism of intermediate stabilization. Sci Rep (2022)

Release Date

2022-03-23

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