SMTL ID : 3e9i.2 (1 other biounit)

Lysyl-tRNA synthetase from Bacillus stearothermophilus complexed with L-Lysine hydroxamate-AMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: E.404, E.411, A.413, N.414 Ligands: XAH.2 No protein-ligand interaction detected (PLIP) MG.5: 5 residues within 4Å: Chain B: E.404, E.411, A.413, N.414 Ligands: XAH.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.404

2 x XAH: 5'-O-{(R)-hydroxy[(L-lysylamino)oxy]phosphoryl}adenosine(Non-covalent)

XAH.2: 27 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, A.415, F.416, E.418, G.463, L.464, G.465, G.467, R.470, I.481 Ligands: MG.1 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:F.416 Hydrogen bonds: A:R.253, A:R.253, A:E.255, A:N.262, A:E.269, A:E.411, A:N.414, A:E.418, A:G.467 Water bridges: A:D.469 Salt bridges: A:R.253 pi-Stacking: A:F.265, A:F.265 pi-Cation interactions: A:R.470 XAH.6: 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, A.415, F.416, E.418, G.463, G.465, G.467, R.470, I.481 Ligands: MG.5 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:F.416 Hydrogen bonds: B:E.231, B:R.253, B:E.255, B:E.255, B:N.262, B:E.269, B:Y.271, B:E.411, B:N.414, B:E.418, B:G.467 Water bridges: B:R.253 Salt bridges: B:R.253 pi-Stacking: B:F.265, B:F.265 pi-Cation interactions: B:R.470

2 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.3: 11 residues within 4Å: Chain A: S.178, L.179, Q.182, S.183, R.186, E.294 Chain B: D.189, S.190, Y.193, L.194, E.195 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:E.195, A:Q.182, A:Q.182 1PE.4: 9 residues within 4Å: Chain A: R.186, D.189, S.190, Y.193, L.194, E.195, Y.246 Chain B: L.179, Q.182 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.182, A:E.195

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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