SMTL ID : 3bju.2 (2 other biounits)

Crystal Structure of tetrameric form of human lysyl-tRNA synthetase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.31 Å

Oligo State

homo-dimer

Ligands

6 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.1: 5 residues within 4Å: Chain A: R.417, E.419, E.426 Ligands: CA.3, ATP.5 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.419, A:E.426, A:E.426, H2O.7, H2O.8 CA.2: 2 residues within 4Å: Chain A: H.263 Ligands: ATP.5 No protein-ligand interaction detected (PLIP) CA.3: 3 residues within 4Å: Chain A: E.426 Ligands: CA.1, ATP.5 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.426, H2O.3, H2O.7, H2O.9 CA.6: 4 residues within 4Å: Chain B: E.419, E.426 Ligands: CA.8, ATP.10 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.419, B:E.426, B:E.426, H2O.16, H2O.18 CA.7: 1 residues within 4Å: Ligands: ATP.10 No protein-ligand interaction detected (PLIP) CA.8: 3 residues within 4Å: Chain B: E.426 Ligands: CA.6, ATP.10 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.426, H2O.16, H2O.17, H2O.18

2 x LYS: LYSINE(Non-covalent)

LYS.4: 14 residues within 4Å: Chain A: G.209, A.210, A.231, E.233, R.255, E.271, Y.273, N.429, Y.431, E.433, G.478, W.479, G.480 Ligands: ATP.5 8 PLIP interactions: 8 interactions with chain A, Hydrophobic interactions: A:Y.431 Hydrogen bonds: A:G.209, A:N.429, A:E.433 Water bridges: A:R.255, A:Y.431, A:Y.431 Salt bridges: A:R.255 LYS.9: 15 residues within 4Å: Chain B: G.209, A.210, A.231, E.233, R.255, E.271, Y.273, N.429, A.430, Y.431, E.433, G.478, W.479, G.480 Ligands: ATP.10 10 PLIP interactions: 9 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:Y.431 Hydrogen bonds: B:G.209, B:E.233, B:Y.273, B:N.429, B:E.433 Water bridges: B:R.255, B:Y.431, K.9 Salt bridges: B:R.255

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.5: 17 residues within 4Å: Chain A: R.255, E.257, T.262, H.263, N.264, F.267, T.269, E.426, I.427, N.429, G.482, R.485, I.496 Ligands: CA.1, CA.2, CA.3, LYS.4 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:E.257, A:E.257, A:N.264, A:E.426, A:E.426, A:N.429, A:G.482 Water bridges: A:R.255, A:R.255, A:R.255, A:R.255, A:R.255, A:E.426, A:D.484, A:R.485 Salt bridges: A:R.255, A:R.255, A:H.263, A:R.485 pi-Stacking: A:F.267, A:F.267 ATP.10: 17 residues within 4Å: Chain B: R.255, E.257, T.262, H.263, N.264, F.267, E.426, I.427, C.428, N.429, G.482, R.485, I.496 Ligands: CA.6, CA.7, CA.8, LYS.9 24 PLIP interactions: 23 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: B:E.257, B:E.257, B:N.264, B:E.426, B:E.426, B:N.429, B:G.482, B:R.485 Water bridges: B:V.211, B:V.211, B:R.255, B:R.255, B:R.255, B:R.255, B:R.255, K.9 Salt bridges: B:R.255, B:R.255, B:H.263, B:R.485 pi-Stacking: B:F.267, B:F.267 pi-Cation interactions: B:R.485, B:R.485

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guo, M. et al., Crystal structure of tetrameric form of human lysyl-tRNA synthetase: Implications for multisynthetase complex formation. Proc.Natl.Acad.Sci.Usa (2008)

Release Date

2008-02-05

Peptides

Lysyl-tRNA synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Lysyl-tRNA synthetase

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