SMTL ID : 9jkl.1

LYSYL-TRNA SYNTHETASE(LysRS) COMPLEXED WITH LYSINE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x LYS: LYSINE(Non-covalent)

LYS.1: 16 residues within 4Å: Chain A: G.237, A.238, A.259, E.261, R.283, M.297, E.299, Y.301, N.444, A.445, F.446, E.448, G.493, L.494, G.495 Ligands: GOL.5 7 PLIP interactions: 7 interactions with chain A, Hydrophobic interactions: A:F.446 Hydrogen bonds: A:G.237, A:E.261, A:Y.301, A:N.444, A:E.448 Salt bridges: A:R.283 LYS.9: 16 residues within 4Å: Chain B: G.237, A.238, A.259, E.261, R.283, M.297, E.299, Y.301, N.444, A.445, F.446, E.448, G.493, L.494, G.495 Ligands: GOL.13 5 PLIP interactions: 5 interactions with chain B, Hydrophobic interactions: B:F.446 Hydrogen bonds: B:G.237, B:N.444, B:E.448 Salt bridges: B:R.283

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: Q.124, V.125, E.129, K.161, K.162 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.124 GOL.3: 5 residues within 4Å: Chain A: H.348, G.411, N.423, E.425, F.429 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.348, A:N.423 Water bridges: A:E.425 GOL.4: 5 residues within 4Å: Chain A: G.358, V.359, D.360, E.363, E.369 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.358, A:D.360 GOL.5: 7 residues within 4Å: Chain A: R.283, M.297, E.441, G.495, G.497 Ligands: LYS.1, GOL.6 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:R.283, A:R.283, A:H.442, A:G.497, K.1 GOL.6: 6 residues within 4Å: Chain A: H.291, N.292, F.295, R.500, I.511 Ligands: GOL.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.292, A:N.292 Water bridges: A:R.500, A:R.500 GOL.7: 3 residues within 4Å: Chain A: K.274 Chain B: R.61, G.63 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.61, B:S.62, A:K.274 Water bridges: B:R.61, B:R.61, B:R.61 GOL.8: 3 residues within 4Å: Chain A: G.222, L.224 Chain B: L.112 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.222 GOL.10: 5 residues within 4Å: Chain B: Q.124, V.125, E.129, K.161, K.162 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.124 GOL.11: 5 residues within 4Å: Chain B: H.348, G.411, N.423, E.425, F.429 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.348, B:N.423 GOL.12: 5 residues within 4Å: Chain B: G.358, V.359, D.360, E.363, E.369 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.358, B:D.360 GOL.13: 7 residues within 4Å: Chain B: R.283, M.297, E.441, G.495, G.497 Ligands: LYS.9, GOL.14 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: B:R.283, B:R.283, B:H.442, B:G.497, K.9 GOL.14: 6 residues within 4Å: Chain B: H.291, N.292, F.295, R.500, I.511 Ligands: GOL.13 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:H.291, B:N.292, B:N.292 Water bridges: B:D.499, B:R.500, B:R.500 GOL.15: 3 residues within 4Å: Chain A: R.61, G.63 Chain B: K.274 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.61, A:S.62, B:K.274 Water bridges: A:R.61, A:R.61, A:R.61 GOL.16: 3 residues within 4Å: Chain A: L.112 Chain B: G.222, L.224 1 PLIP interactions: 1 interactions with chain B Water bridges: B:G.222

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jani, J. et al., LYSYL-TRNA SYNTHETASE(LysRS) COMPLEXED WITH LYSINE. To Be Published

Release Date

2025-09-10

Peptides

Lysine--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Lysine--tRNA ligase