SMTL ID : 6kid.1

Crystal structure of human leucyl-tRNA synthetase, ATP-bound form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.15 Å

Oligo State

monomer

Ligands

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Covalent)

ATP.1: 15 residues within 4Å: Chain A: F.62, P.63, Y.64, P.65, Y.66, G.74, H.75, S.78, E.269, S.685, G.686, D.688, L.689, H.721, L.722 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Y.66, A:G.74, A:S.685, A:G.686, A:L.722 Water bridges: A:H.103 Salt bridges: A:H.263 pi-Cation interactions: A:H.72, A:H.75

1 x LEU: LEUCINE(Non-covalent)

LEU.2: 9 residues within 4Å: Chain A: T.305, L.306, V.401, T.402, S.408, D.410, D.411, K.476, Y.480 9 PLIP interactions: 1 Ligand-Ligand interactions, 8 interactions with chain A Hydrogen bonds: L.2, A:T.305, A:L.306, A:T.402, A:T.402, A:Y.480, A:Y.480 Hydrophobic interactions: A:V.401 Salt bridges: A:K.476

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 4 residues within 4Å: Chain A: Q.266, T.267, G.268, E.269 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.268, A:E.269 Water bridges: A:K.524, A:K.524 PO4.4: 2 residues within 4Å: Chain A: N.68, R.529 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.68 Salt bridges: A:R.529

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, S. et al., Leucine-sensing mechanism of leucyl-tRNA synthetase 1 for mTORC1 activation. Cell Rep (2021)

Release Date

2021-01-27

Peptides

Leucine--tRNA ligase, cytoplasmic: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Leucine--tRNA ligase, cytoplasmic

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