SMTL ID : 9d2r.1

Crystal structure of E. coli Threonine dehydratase regulatory domain in complex with isoleucine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x ILE: ISOLEUCINE(Non-covalent)

ILE.1: 11 residues within 4Å: Chain A: P.32, E.33, E.34, G.36, S.37, F.38, Y.55, A.63, I.65, N.145, I.146 15 PLIP interactions: 15 interactions with chain A, Hydrophobic interactions: A:F.38, A:Y.55, A:Y.55, A:Y.55, A:A.63, A:I.65, A:I.146 Hydrogen bonds: A:G.36, A:S.37, A:F.38, A:N.145, A:I.146 Water bridges: A:E.33, A:L.39, A:N.145 ILE.8: 11 residues within 4Å: Chain B: P.32, E.33, E.34, G.36, S.37, F.38, Y.55, A.63, I.65, N.145, I.146 16 PLIP interactions: 16 interactions with chain B, Hydrophobic interactions: B:F.38, B:Y.55, B:Y.55, B:Y.55, B:A.63, B:I.65, B:I.146 Hydrogen bonds: B:G.36, B:S.37, B:F.38, B:Y.55, B:N.145, B:I.146 Water bridges: B:L.39, B:N.145, B:N.145

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: C.42, L.45, R.48, V.50, F.53, L.133 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:C.42, A:R.48, A:V.50 Water bridges: A:L.133, A:L.133 GOL.3: 1 residues within 4Å: Chain A: E.34 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.34 Water bridges: A:E.34, A:E.34 GOL.4: 8 residues within 4Å: Chain A: Y.55, R.56, A.58, C.64, V.109, G.110 Chain B: R.112, F.197 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.56, A:C.64, A:G.110, B:R.112 Water bridges: A:C.64, A:C.64, A:C.64, B:R.112, B:R.112 GOL.5: 5 residues within 4Å: Chain A: F.57, H.115, L.117, N.145, E.166 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.115 Water bridges: A:E.33, A:E.33, A:E.33, A:N.145 GOL.6: 6 residues within 4Å: Chain A: D.97, D.98, E.99, M.100 Chain B: E.188, N.191 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.97, A:D.98, A:E.99, A:M.100, B:N.191 Water bridges: B:E.188 GOL.9: 6 residues within 4Å: Chain B: C.42, L.45, R.48, V.50, F.53, L.133 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:C.42, B:R.48, B:V.50 Water bridges: B:L.133, B:Y.151 GOL.10: 1 residues within 4Å: Chain B: E.34 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.34 Water bridges: B:E.34, B:E.34 GOL.11: 8 residues within 4Å: Chain A: R.112, F.197 Chain B: Y.55, R.56, A.58, C.64, V.109, G.110 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.56, B:C.64, B:G.110, A:R.112 Water bridges: B:C.64, B:C.64, B:C.64, A:R.112, A:R.112 GOL.12: 5 residues within 4Å: Chain B: F.57, H.115, L.117, N.145, E.166 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.115 Water bridges: B:E.33, B:E.33, B:N.145, B:N.145 GOL.13: 6 residues within 4Å: Chain A: E.188, N.191 Chain B: D.97, D.98, E.99, M.100 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:N.191, B:D.97, B:D.98, B:E.99, B:M.100

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.7: 3 residues within 4Å: Chain A: D.59, N.62, C.64 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:N.62 ACT.14: 3 residues within 4Å: Chain B: D.59, N.62, C.64 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:N.62

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

L-threonine dehydratase biosynthetic IlvA