SMTL ID : 2dlc.1

Crystal structure of the ternary complex of yeast tyrosyl-tRNA synthetase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain B: A.47, T.49, Y.56, Y.101 Ligands: YMP.2 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:A.47, B:Y.56, B:Y.101, YMP.2 MG.3: 5 residues within 4Å: Chain D: A.47, T.49, Y.56, Y.101 Ligands: YMP.4 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Ligand interactions Metal complexes: D:A.47, D:Y.56, D:Y.101, YMP.4

2 x YMP: O-(ADENOSINE-5'-O-YL)-N-(L-TYROSYL)PHOSPHORAMIDATE(Non-covalent)

YMP.2: 26 residues within 4Å: Chain B: Y.43, W.44, G.45, T.46, A.47, H.53, G.55, Y.56, P.59, L.76, A.78, H.81, V.156, Y.170, Q.174, D.177, Q.186, G.188, G.189, D.191, Q.192, N.216, P.217, M.218, V.219 Ligands: MG.1 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:Y.43, B:L.76, B:A.78, B:Q.174, B:Q.174 Hydrogen bonds: B:Y.43, B:Y.43, B:G.45, B:A.47, B:A.47, B:Y.56, B:Y.170, B:Q.174, B:G.189, B:Q.192, B:N.216, B:V.219, B:V.219 pi-Stacking: B:H.81 YMP.4: 26 residues within 4Å: Chain D: Y.43, W.44, G.45, T.46, A.47, H.53, G.55, Y.56, P.59, L.76, A.78, H.81, V.156, Y.170, Q.174, D.177, Q.186, G.188, G.189, D.191, Q.192, N.216, P.217, M.218, V.219 Ligands: MG.3 21 PLIP interactions: 21 interactions with chain D Hydrophobic interactions: D:Y.43, D:L.76, D:A.78, D:Q.174, D:Q.174 Hydrogen bonds: D:Y.43, D:G.45, D:T.46, D:A.47, D:A.47, D:Y.56, D:Y.170, D:Y.170, D:Q.174, D:D.177, D:G.189, D:Q.192, D:N.216, D:V.219, D:V.219 pi-Stacking: D:H.81

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tsunoda, M. et al., Structural basis for recognition of cognate tRNA by tyrosyl-tRNA synthetase from three kingdoms. Nucleic Acids Res. (2007)

Release Date

2007-06-12

Peptides

Tyrosyl-tRNA synthetase, cytoplasmic: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
X

D
X

Tyrosyl-tRNA synthetase, cytoplasmic