SMTL ID : 3bju.1 (2 other biounits)

Crystal Structure of tetrameric form of human lysyl-tRNA synthetase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.31 Å

Oligo State

homo-tetramer

Ligands

12 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 CA.11: 5 residues within 4Å: Chain C: E.419, E.426, N.429 Ligands: CA.13, ATP.15 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.419, C:E.426, C:E.426 CA.12: 2 residues within 4Å: Chain C: H.263 Ligands: ATP.15 No protein-ligand interaction detected (PLIP) CA.13: 3 residues within 4Å: Chain C: E.426 Ligands: CA.11, ATP.15 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.426, H2O.23, H2O.29 CA.16: 4 residues within 4Å: Chain D: E.419, E.426 Ligands: CA.18, ATP.20 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.419, D:E.426, D:E.426 CA.17: 1 residues within 4Å: Ligands: ATP.20 No protein-ligand interaction detected (PLIP) CA.18: 3 residues within 4Å: Chain D: E.426 Ligands: CA.16, ATP.20 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.426, H2O.34, H2O.36, H2O.37

4 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 LYS.14: 14 residues within 4Å: Chain C: 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.15 8 PLIP interactions: 8 interactions with chain C, Hydrophobic interactions: C:Y.431 Hydrogen bonds: C:G.209, C:E.233, C:Y.273, C:N.429, C:E.433 Water bridges: C:R.255 Salt bridges: C:R.255 LYS.19: 15 residues within 4Å: Chain D: 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.20 7 PLIP interactions: 7 interactions with chain D, Hydrophobic interactions: D:Y.431 Hydrogen bonds: D:G.209, D:Y.273, D:N.429 Water bridges: D:R.255, D:E.271 Salt bridges: D:R.255

4 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 ATP.15: 17 residues within 4Å: Chain C: 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.11, CA.12, CA.13, LYS.14 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:E.257, C:N.264, C:E.426, C:E.426, C:N.429, C:G.482 Water bridges: C:R.255, C:R.255, C:R.255, C:R.485, C:R.485 Salt bridges: C:R.255, C:R.255, C:H.263, C:R.485 pi-Stacking: C:F.267, C:F.267 pi-Cation interactions: C:R.485 ATP.20: 17 residues within 4Å: Chain D: 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.16, CA.17, CA.18, LYS.19 20 PLIP interactions: 20 interactions with chain D Hydrogen bonds: D:E.257, D:N.264, D:E.426, D:N.429, D:G.482, D:R.485 Water bridges: D:V.211, D:R.255, D:R.255, D:R.255, D:D.484, D:R.485 Salt bridges: D:R.255, D:R.255, D:H.263, D:R.485 pi-Stacking: D:F.267, D:F.267 pi-Cation interactions: D:R.485, D: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: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Lysyl-tRNA synthetase

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