SMTL ID : 8h9b.1

Crystal structure of chemically modified E. coli ThrS catalytic domain 3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.23 Å

Oligo State

homo-dimer

Ligands

2 x X5V: N-(2,3-dihydroxybenzoyl)-4-(4-nitrophenyl)-L-threonine(Covalent)

X5V.1: 13 residues within 4Å: Chain A: Y.73, A.76, M.92, C.94, R.123, D.143, H.145, K.222, T.242, H.271, R.272, A.273 Ligands: ZN.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:T.242, A:A.273 Hydrogen bonds: A:Y.73 pi-Stacking: A:Y.73 pi-Cation interactions: A:R.123 X5V.3: 13 residues within 4Å: Chain B: Y.73, A.76, M.92, C.94, R.123, D.143, H.145, K.222, T.242, H.271, R.272, A.273 Ligands: ZN.4 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:T.242, B:A.273 Hydrogen bonds: B:Y.73, B:Y.73 pi-Stacking: B:Y.73 pi-Cation interactions: B:R.123

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.94, H.145, H.271 Ligands: X5V.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.94, A:H.145, A:H.271 ZN.4: 4 residues within 4Å: Chain B: C.94, H.145, H.271 Ligands: X5V.3 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
A

Threonine--tRNA ligase

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