SMTL ID : 3e9h.2 (1 other biounit)

Lysyl-tRNA synthetase from Bacillus stearothermophilus complexed with L-Lysylsulfamoyl adenosine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: R.402, E.404, E.411, N.414 Ligands: KAA.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.404, A:E.411 MG.3: 5 residues within 4Å: Chain B: R.402, E.404, E.411, N.414 Ligands: KAA.4 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.404, B:E.411

2 x KAA: 5'-O-[(L-LYSYLAMINO)SULFONYL]ADENOSINE(Non-covalent)

KAA.2: 26 residues within 4Å: Chain A: G.207, A.208, A.229, E.231, R.253, E.255, R.260, H.261, N.262, F.265, M.267, E.269, Y.271, E.411, H.412, A.413, N.414, F.416, E.418, G.463, L.464, G.465, G.467, R.470, I.481 Ligands: MG.1 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:F.416 Hydrogen bonds: A:R.253, A:E.255, A:N.262, A:E.269, A:E.411, A:E.411, A:A.413, A:N.414, A:E.418, A:G.467, A:R.470 Water bridges: A:R.253, A:R.253, A:R.253, A:D.469 Salt bridges: A:R.253 pi-Stacking: A:F.265, A:F.265 KAA.4: 26 residues within 4Å: Chain B: G.207, A.208, A.229, E.231, R.253, E.255, R.260, H.261, N.262, F.265, M.267, E.269, Y.271, E.411, H.412, A.413, N.414, F.416, E.418, G.463, L.464, G.465, G.467, R.470, I.481 Ligands: MG.3 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:F.416 Hydrogen bonds: B:E.231, B:R.253, B:E.255, B:N.262, B:N.262, B:E.269, B:Y.271, B:Y.271, B:E.411, B:E.411, B:N.414, B:G.467, B:R.470 Water bridges: B:R.253, B:R.253 Salt bridges: B:R.253 pi-Stacking: B:F.265, B:F.265

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sakurama, H. et al., Two crystal structures of lysyl-tRNA synthetase from Bacillus stearothermophilus in complex with lysyladenylate-like compounds: insights into the irreversible formation of the enzyme-bound adenylate of L-lysine hydroxamate. J.Biochem. (2009)

Release Date

2009-07-14

Peptides

Lysyl-tRNA synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Lysyl-tRNA synthetase

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