SMTL ID : 9d2q.1

Crystal structure of E. coli Threonine dehydratase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

homo-tetramer

Ligands

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 10 residues within 4Å: Chain A: E.366, E.367, K.368, G.369, S.370, F.371, Y.388, W.477, N.478, I.479 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.366, A:G.369, A:N.478, A:I.479 Water bridges: A:G.369, A:F.371, A:Y.388 GOL.2: 7 residues within 4Å: Chain A: L.243, C.274, Q.275, L.278, D.279, D.280, I.281 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.275, A:D.280, A:D.280 GOL.5: 6 residues within 4Å: Chain A: D.285, S.286, D.287, R.349 Chain B: E.458, R.493 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:E.458, B:E.458, B:R.493, A:D.285, A:S.286, A:D.287, A:R.349 GOL.6: 10 residues within 4Å: Chain B: E.366, E.367, K.368, G.369, S.370, F.371, Y.388, W.477, N.478, I.479 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:E.366, B:G.369, B:N.478, B:I.479 Water bridges: B:G.369, B:F.371, B:Y.388 GOL.7: 7 residues within 4Å: Chain B: L.243, C.274, Q.275, L.278, D.279, D.280, I.281 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.275, B:D.280, B:D.280 GOL.10: 6 residues within 4Å: Chain A: E.458, R.493 Chain B: D.285, S.286, D.287, R.349 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:D.285, B:S.286, B:D.287, B:R.349, A:E.458, A:E.458, A:R.493 GOL.11: 10 residues within 4Å: Chain C: E.366, E.367, K.368, G.369, S.370, F.371, Y.388, W.477, N.478, I.479 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:E.366, C:G.369, C:N.478, C:I.479 Water bridges: C:G.369, C:F.371 GOL.12: 7 residues within 4Å: Chain C: L.243, C.274, Q.275, L.278, D.279, D.280, I.281 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.275, C:D.280 GOL.15: 6 residues within 4Å: Chain C: D.285, S.286, D.287, R.349 Chain D: E.458, R.493 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:D.285, C:S.286, C:D.287, C:R.349, D:E.458, D:E.458, D:R.493 GOL.16: 10 residues within 4Å: Chain D: E.366, E.367, K.368, G.369, S.370, F.371, Y.388, W.477, N.478, I.479 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:E.366, D:G.369, D:N.478, D:I.479 Water bridges: D:G.369, D:F.371 GOL.17: 7 residues within 4Å: Chain D: L.243, C.274, Q.275, L.278, D.279, D.280, I.281 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.275, D:D.280 GOL.20: 6 residues within 4Å: Chain C: E.458, R.493 Chain D: D.285, S.286, D.287, R.349 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:D.285, D:S.286, D:D.287, D:R.349, C:E.458, C:E.458, C:R.493

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

PGE.3: 7 residues within 4Å: Chain A: Y.45, V.50, E.191, Q.194, Q.195 Chain D: Q.194 Ligands: PGE.18 No protein-ligand interaction detected (PLIP) PGE.8: 7 residues within 4Å: Chain B: Y.45, V.50, E.191, Q.194, Q.195 Chain C: Q.194 Ligands: PGE.13 No protein-ligand interaction detected (PLIP) PGE.13: 7 residues within 4Å: Chain B: Q.194 Chain C: Y.45, V.50, E.191, Q.194, Q.195 Ligands: PGE.8 No protein-ligand interaction detected (PLIP) PGE.18: 7 residues within 4Å: Chain A: Q.194 Chain D: Y.45, V.50, E.191, Q.194, Q.195 Ligands: PGE.3 No protein-ligand interaction detected (PLIP)

4 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.4: 4 residues within 4Å: Chain A: F.154, E.259, A.262, V.263 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.136, A:K.264 Salt bridges: A:E.259, A:E.259 EPE.9: 4 residues within 4Å: Chain B: F.154, E.259, A.262, V.263 4 PLIP interactions: 4 interactions with chain B Water bridges: B:K.136, B:K.264 Salt bridges: B:E.259, B:E.259 EPE.14: 4 residues within 4Å: Chain C: F.154, E.259, A.262, V.263 4 PLIP interactions: 4 interactions with chain C Water bridges: C:K.136, C:K.264 Salt bridges: C:E.259, C:E.259 EPE.19: 4 residues within 4Å: Chain D: F.154, E.259, A.262, V.263 4 PLIP interactions: 4 interactions with chain D Water bridges: D:K.136, D:K.264 Salt bridges: D:E.259, D:E.259

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yun, M.D. et al., Isoleucine binding and regulation of Escherichia coli and Staphylococcus aureus threonine dehydratase (IlvA). Biorxiv (2025)

Release Date

2025-04-09

Peptides

L-threonine dehydratase biosynthetic IlvA: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

L-threonine dehydratase biosynthetic IlvA