SMTL ID : 9sh9.1

Thermus thermophilus asparaginyl-tRNA synthetase dimer with bound ATP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.95 Å

Oligo State

homo-dimer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: R.208, E.210 Ligands: ATP.4 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.210 MG.2: 3 residues within 4Å: Chain A: D.352, E.361 Ligands: ATP.4 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.361 MG.3: 3 residues within 4Å: Chain A: E.313, E.361 Ligands: ATP.4 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.361 MG.5: 3 residues within 4Å: Chain B: R.208, E.210 Ligands: ATP.8 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.210 MG.6: 3 residues within 4Å: Chain B: D.352, E.361 Ligands: ATP.8 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.361 MG.7: 4 residues within 4Å: Chain B: R.216, E.313, E.361 Ligands: ATP.8 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.361

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.4: 17 residues within 4Å: Chain A: R.208, E.210, R.216, H.217, L.218, F.221, M.223, E.361, I.362, I.363, G.364, G.407, G.409, R.412 Ligands: MG.1, MG.2, MG.3 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:L.218, A:L.218, A:E.361, A:E.361, A:E.361, A:G.409 Salt bridges: A:R.208, A:R.208, A:R.216, A:H.217, A:R.412 pi-Stacking: A:F.221 pi-Cation interactions: A:R.412 ATP.8: 17 residues within 4Å: Chain B: R.208, E.210, R.216, H.217, L.218, F.221, M.223, E.361, I.362, I.363, G.364, G.407, G.409, R.412 Ligands: MG.5, MG.6, MG.7 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:L.218, B:L.218, B:E.361, B:I.363, B:G.409 Salt bridges: B:R.208, B:R.208, B:R.216, B:H.217, B:R.412 pi-Stacking: B:F.221, B:F.221 pi-Cation interactions: B:R.412

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Berthet-Colominas, C. et al., The crystal structure of asparaginyl-tRNA synthetase from Thermus thermophilus and its complexes with ATP and asparaginyl-adenylate: the mechanism of discrimination between asparagine and aspartic acid. EMBO J (1998)

Release Date

2025-09-17

Peptides

Asparagine--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Asparagine--tRNA ligase

Related Entries With Identical Sequence