SMTL ID : 8wii.1

Crystal structure of E. coli ThrS catalytic domain mutant G463A in complex with Obafluorin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.98 Å

Oligo State

homo-dimer

Ligands

2 x WE3: ~{N}-[(2~{R},3~{S})-2-[(4-nitrophenyl)methyl]-4-oxidanylidene-oxetan-3-yl]-2,3-bis(oxidanyl)benzamide(Non-covalent)

WE3.1: 15 residues within 4Å: Chain A: M.92, C.94, R.123, M.134, V.136, F.139, D.143, H.145, T.242, Q.244, H.271, R.272, A.273, S.277 Ligands: ZN.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:T.242, A:H.271, A:A.273 Hydrogen bonds: A:Q.244, A:S.277 Salt bridges: A:R.123, A:K.225 pi-Stacking: A:F.139 WE3.3: 17 residues within 4Å: Chain B: C.94, M.134, F.139, Q.141, D.143, H.145, K.225, Q.239, T.242, Q.244, H.271, R.272, A.273, G.276, S.277, R.280 Ligands: ZN.4 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.139, B:H.271, B:A.273 Hydrogen bonds: B:Q.141, B:Q.244, B:S.277 Salt bridges: B:K.225

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.94, H.145, H.271 Ligands: WE3.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.94, A:H.145, A:H.271 ZN.4: 6 residues within 4Å: Chain B: C.94, D.143, H.145, Q.244, H.271 Ligands: WE3.3 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., Specific glycine-dependent enzyme motion determines the potency of conformation selective inhibitors of threonyl-tRNA synthetase. Commun Biol (2024)

Release Date

2024-07-24

Peptides

Threonine--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Threonine--tRNA ligase

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