SMTL ID : 9sh8.1

Thermus thermophilus asparaginyl-tRNA synthetase with bound sulphamoyl-analogue of asparaginyl-adenylate (AsnAMS)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.62 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: K.334, D.352, E.361 Ligands: NSS.2 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.361, H2O.1 MG.3: 4 residues within 4Å: Chain B: K.334, D.352, E.361 Ligands: NSS.4 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.361, H2O.3

2 x NSS: 5'-O-[N-(L-ASPARAGINYL)SULFAMOYL]ADENOSINE(Non-covalent)

NSS.2: 22 residues within 4Å: Chain A: E.164, S.185, Q.187, R.208, R.216, H.217, L.218, F.221, M.223, E.225, Y.337, E.361, I.362, I.363, G.364, R.368, G.405, F.406, G.407, G.409, R.412 Ligands: MG.1 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:E.164, A:S.185, A:R.208, A:L.218, A:L.218, A:E.225, A:E.361, A:R.368, A:R.368, A:G.407, A:G.409, A:R.412 Salt bridges: A:R.208 pi-Stacking: A:F.221, A:F.221 pi-Cation interactions: A:R.412, A:R.412 NSS.4: 22 residues within 4Å: Chain B: E.164, S.185, Q.187, R.208, R.216, H.217, L.218, F.221, M.223, E.225, Y.337, E.361, I.362, I.363, G.364, R.368, G.405, F.406, G.407, G.409, R.412 Ligands: MG.3 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:E.164, B:S.185, B:R.208, B:L.218, B:L.218, B:E.225, B:E.225, B:Y.337, B:E.361, B:R.368, B:R.368, B:G.407, B:G.409, B:R.412 Salt bridges: B:R.208 pi-Stacking: B:F.221, B:F.221 pi-Cation interactions: B:R.412, 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
A

Asparagine--tRNA ligase

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