SMTL ID : 9qof.1

E.coli seryl-tRNA synthetase (Arm deletion mutant) bound to sulphamoyl seryl-adenylate analogue

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.32 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: E.293, S.296 Ligands: SSA.3 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.293, H2O.3, H2O.6 MG.4: 2 residues within 4Å: Chain B: E.293 Ligands: SSA.6 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.293, H2O.10, H2O.11

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

SO4.2: 4 residues within 4Å: Chain A: R.221, R.292, E.293, R.335 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.293, A:E.293 Water bridges: A:E.293, A:E.293 Salt bridges: A:R.221, A:R.292, A:R.335 SO4.5: 4 residues within 4Å: Chain B: R.221, R.292, E.293, R.335 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.293 Water bridges: B:R.292, B:R.292 Salt bridges: B:R.221, B:R.292, B:R.335

2 x SSA: 5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE(Non-covalent)

SSA.3: 21 residues within 4Å: Chain A: T.175, E.177, R.206, E.208, L.219, I.220, R.221, M.222, F.225, K.227, E.229, E.293, I.294, S.295, S.296, N.327, G.328, S.329, A.332, R.335 Ligands: MG.1 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:T.175, A:T.175, A:E.177, A:R.206, A:E.208, A:M.222, A:K.227, A:E.293, A:S.329, A:R.335, A:R.335 Water bridges: A:R.206, A:S.296 Salt bridges: A:R.206 pi-Stacking: A:F.225, A:F.225 SSA.6: 20 residues within 4Å: Chain B: T.175, E.177, R.206, E.208, I.220, R.221, M.222, F.225, K.227, E.229, E.293, I.294, S.295, S.296, N.327, G.328, S.329, A.332, R.335 Ligands: MG.4 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:T.175, B:T.175, B:E.177, B:R.206, B:E.208, B:M.222, B:K.227, B:E.293, B:E.293, B:S.329, B:R.335, B:R.335 Water bridges: B:S.296, B:S.296 Salt bridges: B:R.206 pi-Stacking: B:F.225, B:F.225

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Borel, F. et al., Seryl-tRNA synthetase from Escherichia coli,implication of its N-terminal domain in aminoacylation activity and specificity. Nucleic Acids Res (1994)

Release Date

2025-05-14

Peptides

Serine--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Serine--tRNA ligase