SMTL ID : 1j1u.1

Crystal structure of archaeal tyrosyl-tRNA synthetase complexed with tRNA(Tyr) and L-tyrosine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

8 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: A.9, G.10, U.48 No protein-ligand interaction detected (PLIP) MG.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.4: 1 residues within 4Å: Chain B: H.160 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.160, H2O.14, H2O.14 MG.6: 3 residues within 4Å: Chain C: A.9, G.10, U.48 No protein-ligand interaction detected (PLIP) MG.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.9: 1 residues within 4Å: Chain D: H.160 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.160, H2O.28, H2O.28

2 x TYR: TYROSINE(Non-covalent)

TYR.5: 10 residues within 4Å: Chain B: Y.32, G.34, E.36, L.65, A.67, H.70, Y.151, Q.155, D.158, Q.173 13 PLIP interactions: 12 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:Y.32, B:L.65, B:A.67 Hydrogen bonds: B:E.36, B:Y.151, B:Q.155, B:Q.155, B:D.158, B:D.158, B:Q.173, B:Q.173, Y.5 pi-Stacking: B:H.70 TYR.10: 10 residues within 4Å: Chain D: Y.32, G.34, E.36, L.65, A.67, H.70, Y.151, Q.155, D.158, Q.173 12 PLIP interactions: 11 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: D:Y.32, D:L.65, D:A.67 Hydrogen bonds: D:Y.32, D:E.36, D:Q.155, D:Q.155, D:D.158, D:Q.173, D:Q.173, Y.10 pi-Stacking: D:H.70

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kobayashi, T. et al., Structural basis for orthogonal tRNA specificities of tyrosyl-tRNA synthetases for genetic code expansion. NAT.STRUCT.BIOL. (2003)

Release Date

2003-06-03

Peptides

Tyrosyl-tRNA synthetase: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
A

D
A

Tyrosyl-tRNA synthetase

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