SMTL ID : 8por.1

Crystal structure of wolbachia leucyl-tRNA synthetase editing domain bound to cmpd6-AMP adduct

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 3 residues within 4Å: Chain A: K.14, V.16, G.17 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.17, A:L.18 Salt bridges: A:K.14

1 x EYT: [(1~{R},5~{S},6~{R},8~{R},9'~{S})-9'-(aminomethyl)-8-(6-aminopurin-9-yl)-2'-bromanyl-5'-[3-oxidanylidene-3-(1,3-thiazol-2-ylamino)propoxy]spiro[2,4,7-trioxa-3-boranuidabicyclo[3.3.0]octane-3,7'-8-oxa-7-boranuidabicyclo[4.3.0]nona-1(6),2,4-triene]-6-yl]methyl dihydrogen phosphate(Non-covalent)

EYT.2: 18 residues within 4Å: Chain A: F.25, T.26, T.27, C.28, T.31, F.96, V.97, L.98, Y.101, R.102, G.104, I.106, F.107, C.109, H.112, D.113, R.115, D.116 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:T.27, A:T.27, A:L.98, A:L.98, A:Y.101, A:Y.101, A:G.104, A:D.113, A:R.115, A:R.115, A:D.116 Water bridges: A:F.25, A:R.102, A:R.102, A:E.103, A:F.107 Salt bridges: A:R.102

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

EDO.3: 3 residues within 4Å: Chain A: Y.75, N.79, P.90 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.79

1 x PE4: 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL(Non-functional Binders)

PE4.4: 5 residues within 4Å: Chain A: A.111, H.112, D.113, Q.114, R.115 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.114, A:Q.114

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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