SMTL ID : 8wnd.1

Crystal structure of Saccharomyces cerevisiae isoleucyl-tRNA synthetase in complex with tRNA(Ile) and isoleucine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

2 x ILE: ISOLEUCINE(Non-covalent)

ILE.1: 10 residues within 4Å: Chain A: G.45, P.46, P.47, F.48, D.85, W.529, S.532, E.561, Q.565, W.569 9 PLIP interactions: 8 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:P.46, A:W.529, A:E.561, A:W.569 Hydrogen bonds: A:P.46, A:F.48, A:D.85, A:Q.565, I.1 ILE.8: 10 residues within 4Å: Chain C: G.45, P.46, P.47, F.48, D.85, W.529, S.532, E.561, Q.565, W.569 9 PLIP interactions: 9 interactions with chain C, Hydrophobic interactions: C:P.46, C:W.529, C:E.561, C:W.569 Hydrogen bonds: C:F.48, C:D.85, C:D.85, C:Q.565, C:Q.565

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

EDO.2: 4 residues within 4Å: Chain A: N.557, K.587, N.588, Y.714 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.588, A:Y.714, A:Y.714

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

SO4.3: 3 residues within 4Å: Chain A: F.48, T.50, R.403 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:T.50 Water bridges: A:F.48, I.1 Salt bridges: A:R.403 SO4.4: 4 residues within 4Å: Chain A: K.176, K.421, R.454, D.455 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.455 Salt bridges: A:K.176 SO4.5: 3 residues within 4Å: Chain A: R.495 Chain C: P.789, E.790 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:E.790 Salt bridges: A:R.495 SO4.6: 3 residues within 4Å: Chain A: K.636, K.715, Y.717 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.717, A:Y.717 Water bridges: A:K.636 Salt bridges: A:K.636, A:K.715 SO4.7: 3 residues within 4Å: Chain A: G.747, V.748, E.749 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.748, A:E.749 Water bridges: A:D.750 SO4.9: 3 residues within 4Å: Chain C: F.48, T.50, R.403 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.50 Salt bridges: C:R.403 SO4.10: 3 residues within 4Å: Chain C: K.421, R.454, D.455 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.455, C:D.455 SO4.11: 3 residues within 4Å: Chain A: P.789, E.790 Chain C: R.495 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:E.790 Salt bridges: C:R.495 SO4.12: 4 residues within 4Å: Chain C: R.767, Y.796, P.809, V.810 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:V.810, C:V.810 Salt bridges: C:R.767

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, B. et al., The eukaryote-specific mechanism for isoleucyl-tRNA synthetase achieving necessary tRNA discrimination. To Be Published

Release Date

2024-10-09

Peptides

isoleucine--tRNA ligase: AC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
B

isoleucine--tRNA ligase