SMTL ID : 8h99.1

Crystal structure of E. coli ThrS catalytic domain mutant

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

homo-dimer

Ligands

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 17 residues within 4Å: Chain A: R.123, E.125, M.134, R.135, V.136, F.139, Q.141, K.225, Q.239, C.240, T.242, Q.244, G.276, S.277, R.280 Ligands: MG.3, MG.4 32 PLIP interactions: 32 interactions with chain A Hydrogen bonds: A:E.125, A:R.135, A:V.136, A:Q.141, A:Q.239, A:Q.239, A:T.242, A:Q.244, A:S.277, A:S.277, A:R.280, A:R.280 Water bridges: A:Y.73, A:Y.73, A:R.123, A:R.123, A:R.123, A:R.123, A:R.135, A:R.135, A:R.135, A:K.225 Salt bridges: A:R.123, A:R.123, A:R.135, A:K.225, A:K.225, A:R.280 pi-Stacking: A:F.139, A:F.139 pi-Cation interactions: A:R.280, A:R.280 ATP.6: 17 residues within 4Å: Chain B: R.123, E.125, M.134, R.135, V.136, F.139, Q.141, K.225, Q.239, C.240, T.242, Q.244, G.276, S.277, R.280 Ligands: MG.8, MG.9 34 PLIP interactions: 34 interactions with chain B Hydrogen bonds: B:E.125, B:R.135, B:V.136, B:Q.141, B:Q.239, B:Q.239, B:Q.239, B:Q.244, B:S.277, B:S.277, B:R.280, B:R.280 Water bridges: B:Y.73, B:R.123, B:R.123, B:R.123, B:R.123, B:R.123, B:R.123, B:R.135, B:R.135, B:R.135, B:K.225, B:Q.244 Salt bridges: B:R.123, B:R.123, B:R.135, B:K.225, B:K.225, B:R.280 pi-Stacking: B:F.139, B:F.139 pi-Cation interactions: B:R.280, B:R.280

2 x IMD: IMIDAZOLE(Non-covalent)

IMD.2: 6 residues within 4Å: Chain A: C.94, D.143, H.145, Q.244, H.271 Ligands: ZN.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.244 IMD.7: 7 residues within 4Å: Chain B: M.92, C.94, D.143, H.145, Q.244, H.271 Ligands: ZN.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.244 Water bridges: B:Q.141

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: Q.239 Ligands: ATP.1 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain A: R.123 Ligands: ATP.1 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain B: Q.239 Ligands: ATP.6 No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain B: R.123 Ligands: ATP.6 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.5: 4 residues within 4Å: Chain A: C.94, H.145, H.271 Ligands: IMD.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.94, A:H.145, A:H.271 ZN.10: 4 residues within 4Å: Chain B: C.94, H.145, H.271 Ligands: IMD.7 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.94, B:H.145, B:H.271

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Qiao, H. et al., Tyrosine-targeted covalent inhibition of a tRNA synthetase aided by zinc ion. Commun Biol (2023)

Release Date

2023-02-08

Peptides

Threonine--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Threonine--tRNA ligase