SMTL ID : 8ou8.1

Crystal structure of E. coli threonyl tRNA synthetase in complex with a TM84 analogue

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

2 x W0U: [(2~{S},4~{S},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-oxolan-2-yl]methoxy-~{N}-[(2~{S},3~{S})-2-azanyl-3-oxidanyl-butanoyl]phosphonamidic acid(Non-covalent)

W0U.1: 24 residues within 4Å: Chain A: M.93, C.95, R.124, E.126, M.135, R.136, V.137, F.140, Q.142, D.144, H.146, Y.223, K.226, Q.240, C.241, T.243, Q.245, H.272, R.273, A.274, G.277, S.278, R.281 Ligands: ZN.3 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:A.274 Hydrogen bonds: A:R.124, A:R.124, A:E.126, A:V.137, A:Q.142, A:Y.223, A:K.226, A:K.226, A:Q.240, A:Q.245, A:S.278, A:R.281 Water bridges: A:D.144, A:R.281, A:R.281 pi-Stacking: A:F.140, A:F.140 pi-Cation interactions: A:R.281 W0U.5: 23 residues within 4Å: Chain B: M.93, C.95, R.124, E.126, M.135, R.136, V.137, F.140, Q.142, D.144, H.146, Y.223, K.226, Q.240, C.241, T.243, Q.245, H.272, A.274, G.277, S.278, R.281 Ligands: ZN.8 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:A.274 Hydrogen bonds: B:R.124, B:R.124, B:E.126, B:E.126, B:V.137, B:Q.142, B:Y.223, B:K.226, B:K.226, B:Q.240, B:T.243, B:Q.245, B:S.278, B:R.281, B:R.281 Water bridges: B:N.94, B:D.144, B:R.281 pi-Stacking: B:F.140, B:F.140 pi-Cation interactions: B:R.281

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.2: 10 residues within 4Å: Chain A: I.189, M.194, W.195, A.198, Y.223, G.224, L.246, D.247, F.248, S.249 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.248 pi-Cation interactions: A:W.195 DMS.6: 10 residues within 4Å: Chain B: I.189, M.194, W.195, A.198, Y.223, P.225, L.246, D.247, F.248, S.249 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.249 pi-Cation interactions: B:W.195

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: C.95, H.146, H.272 Ligands: W0U.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.95, A:H.146, A:H.272 ZN.8: 4 residues within 4Å: Chain B: C.95, H.146, H.272 Ligands: W0U.5 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.95, B:H.146, B:H.272

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

EDO.4: 3 residues within 4Å: Chain A: E.39, K.55 Chain B: E.39 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.39 EDO.7: 4 residues within 4Å: Chain B: F.35, S.121, T.141, E.280 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.123, B:T.141, B:E.280

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Buitrago, J.A.R. et al., Synthesis and evaluation of an agrocin 84 toxic moiety (TM84) analogue as a malarial threonyl tRNA synthetase inhibitor. Org.Biomol.Chem. (2023)

Release Date

2023-07-12

Peptides

Threonine--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
A

Threonine--tRNA ligase

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