SMTL ID : 8pot.1

Ternary complex of E. coli leucyl-tRNA synthetase, tRNA(leu) and the benzoxaborole cmpd9 in the editing conformation

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

monomer

Ligands

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 6 residues within 4Å: Chain A: Q.35, W.38, D.39, K.133, F.137, W.141 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.35, A:F.137 Water bridges: A:Y.139 EDO.2: 8 residues within 4Å: Chain A: F.668, A.669, S.670, N.743 Chain B: G.12, G.13, A.23, C.24 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.669, A:N.743

1 x 7RZ: [(1R,3'S,5S,6R,8R)-3'-(aminomethyl)-8-(6-aminopurin-9-yl)-4'-bromanyl-7'-[3-[methyl-(phenylmethyl)amino]propoxy]spiro[2,4,7-trioxa-3$l^{4}-borabicyclo[3.3.0]octane-3,1'-3H-2,1$l^{4}-benzoxaborole]-6-yl]methyl dihydrogen phosphate(Non-covalent)

7RZ.3: 19 residues within 4Å: Chain A: S.247, Y.266, T.267, T.268, R.269, T.272, F.345, V.346, L.347, Y.350, V.355, M.356, V.358, H.361, D.362, R.364, D.365 Chain B: C.85, C.86 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:R.269, A:R.269, A:D.362 Hydrogen bonds: A:S.247, A:Y.266, A:T.267, A:T.268, A:T.268, A:L.347, A:L.347, A:V.358, A:D.362, A:R.364, A:R.364, A:D.365 Water bridges: A:Y.266, A:Y.350, A:Y.350, A:A.354, A:M.356

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hoffmann, G. et al., Targeting a microbiota Wolbachian aminoacyl-tRNA synthetase to block its pathogenic host. Sci Adv (2024)

Release Date

2024-06-12

Peptides

Leucine--tRNA ligase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Leucine--tRNA ligase

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