SMTL ID : 6kie.1

Crystal structure of human leucyl-tRNA synthetase, Leu-AMS-bound form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.15 Å

Oligo State

monomer

Ligands

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

PO4.1: 2 residues within 4Å: Chain A: T.267, G.268 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.268 PO4.2: 3 residues within 4Å: Chain A: S.730, K.731, S.732 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.731, A:S.732 PO4.3: 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

1 x LSS: 5'-O-(L-leucylsulfamoyl)adenosine(Covalent)

LSS.4: 22 residues within 4Å: Chain A: F.62, P.63, Y.64, P.65, Y.66, H.72, G.74, H.75, S.78, H.103, H.263, L.606, S.609, R.683, S.685, G.686, D.688, L.689, H.693, G.720, H.721, L.722 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.64, A:L.606 Hydrogen bonds: A:Y.64, A:P.65, A:Y.66, A:H.103, A:S.685, A:G.686, A:D.688, A:L.722 Salt bridges: A:H.75 pi-Cation interactions: A:H.721

1 x LEU: LEUCINE(Non-covalent)

LEU.5: 9 residues within 4Å: Chain A: T.305, L.306, R.307, V.401, T.402, S.408, D.411, K.476, Y.480 8 PLIP interactions: 7 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:V.401 Hydrogen bonds: A:L.306, A:R.307, A:Y.480, A:Y.480, A:Y.480, L.5 Salt bridges: A:K.476

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