SMTL ID : 3a74.1 (1 other biounit)

Lysyl-tRNA synthetase from Bacillus stearothermophilus complexed with Diadenosine Tetraphosphate (AP4A)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x B4P: BIS(ADENOSINE)-5'-TETRAPHOSPHATE(Non-covalent)

B4P.1: 22 residues within 4Å: Chain A: R.253, E.255, G.256, S.258, R.260, H.261, N.262, F.265, M.267, E.366, E.370, E.411, H.412, A.413, N.414, G.467, R.470, I.481 Ligands: LYN.2, MG.3, MG.4, MG.5 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:R.253, A:E.255, A:G.256, A:R.260, A:N.262, A:E.411, A:N.414, A:G.467, A:R.470 Water bridges: A:R.402, A:E.404 Salt bridges: A:R.253, A:R.253, A:H.261, A:R.470 pi-Stacking: A:H.261, A:H.261, A:F.265, A:F.265 pi-Cation interactions: A:R.470 B4P.6: 22 residues within 4Å: Chain B: R.253, E.255, G.256, S.258, R.260, H.261, N.262, F.265, M.267, E.366, E.370, E.411, H.412, A.413, N.414, G.467, R.470, I.481 Ligands: LYN.7, MG.8, MG.9, MG.10 23 PLIP interactions: 23 interactions with chain B Hydrogen bonds: B:R.253, B:E.255, B:E.255, B:G.256, B:R.260, B:N.262, B:E.411, B:N.414, B:G.467, B:R.470 Water bridges: B:R.402, B:E.411, B:D.469, B:R.470 Salt bridges: B:R.253, B:R.253, B:H.261, B:R.470 pi-Stacking: B:H.261, B:F.265, B:F.265 pi-Cation interactions: B:H.261, B:R.470

2 x LYN: 2,6-DIAMINO-HEXANOIC ACID AMIDE(Non-covalent)

LYN.2: 15 residues within 4Å: Chain A: G.207, A.208, A.229, E.231, R.253, M.267, E.269, Y.271, N.414, A.415, F.416, E.418, G.463, G.465 Ligands: B4P.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.416 Hydrogen bonds: A:E.231, A:R.253, A:E.269, A:Y.271, A:N.414, A:E.418 Water bridges: A:G.207, A:A.209, A:E.231 LYN.7: 15 residues within 4Å: Chain B: G.207, A.208, A.229, E.231, R.253, M.267, E.269, Y.271, N.414, A.415, F.416, E.418, G.463, G.465 Ligands: B4P.6 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.416 Hydrogen bonds: B:R.253, B:E.269, B:N.414, B:E.418 Water bridges: B:G.207, B:A.209

6 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: E.404, E.411, A.413, N.414 Ligands: B4P.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.404, A:E.411 MG.4: 2 residues within 4Å: Chain A: R.253 Ligands: B4P.1 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain A: E.404, E.411 Ligands: B4P.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.404, A:E.411, H2O.9 MG.8: 5 residues within 4Å: Chain B: E.404, E.411, A.413, N.414 Ligands: B4P.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.411 MG.9: 2 residues within 4Å: Chain B: R.253 Ligands: B4P.6 No protein-ligand interaction detected (PLIP) MG.10: 3 residues within 4Å: Chain B: E.404, E.411 Ligands: B4P.6 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.404, B:E.411, H2O.16

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sakurama, H. et al., Crystal Structure of Lysyl-tRNA Synthetase from Bacillus stearothermophilus in Complex with Diadenosine Tetraphosphate (AP4A): Insights into AP4A Synthesis Mechanisms and Implication for Recognition of Discriminator Base of tRNA^Lys. To be Published

Release Date

2010-09-22

Peptides

Lysyl-tRNA synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Lysyl-tRNA synthetase

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