SMTL ID : 1e24.1

LYSYL-TRNA SYNTHETASE (LYSU) HEXAGONAL FORM COMPLEXED WITH LYSINE AND ATP AND MN2+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-dimer

Ligands

2 x LYS: LYSINE(Non-covalent)

LYS.1: 13 residues within 4Å: Chain A: G.216, A.217, A.238, E.240, R.262, E.278, Y.280, N.424, F.426, E.428, G.473, G.475 Ligands: ATP.2 9 PLIP interactions: 9 interactions with chain A, Hydrophobic interactions: A:F.426 Hydrogen bonds: A:G.216, A:E.240, A:E.278, A:Y.280, A:N.424, A:E.428 Water bridges: A:R.262 Salt bridges: A:R.262 LYS.8: 13 residues within 4Å: Chain B: G.216, A.217, A.238, E.240, R.262, E.278, Y.280, N.424, F.426, E.428, G.473, G.475 Ligands: ATP.9 6 PLIP interactions: 6 interactions with chain B, Hydrophobic interactions: B:F.426 Hydrogen bonds: B:G.216, B:N.424, B:E.428 Water bridges: B:R.262 Salt bridges: B:R.262

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

ATP.2: 20 residues within 4Å: Chain A: R.262, E.264, R.269, H.270, N.271, F.274, M.276, E.380, E.414, E.421, I.422, G.423, N.424, G.477, R.480, I.491 Ligands: LYS.1, MN.3, MN.4, MN.5 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:R.262, A:E.264, A:E.264, A:N.271, A:E.421, A:E.421, A:N.424, A:G.477 Water bridges: A:R.269, A:R.480 Salt bridges: A:R.262, A:H.270, A:R.480 pi-Stacking: A:F.274, A:F.274 pi-Cation interactions: A:R.480, A:R.480 ATP.9: 20 residues within 4Å: Chain B: R.262, E.264, R.269, H.270, N.271, F.274, M.276, E.380, E.414, E.421, I.422, G.423, N.424, G.477, R.480, I.491 Ligands: LYS.8, MN.10, MN.11, MN.12 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:R.262, B:E.264, B:N.271, B:E.421, B:E.421, B:N.424, B:G.477 Water bridges: B:R.269, B:D.479, B:R.480 Salt bridges: B:R.262, B:H.270, B:R.480 pi-Stacking: B:F.274, B:F.274 pi-Cation interactions: B:R.480, B:R.480

6 x MN: MANGANESE (II) ION(Non-covalent)

MN.3: 4 residues within 4Å: Chain A: E.414, E.421 Ligands: ATP.2, MN.5 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.414, A:E.421 MN.4: 2 residues within 4Å: Chain A: H.270 Ligands: ATP.2 No protein-ligand interaction detected (PLIP) MN.5: 4 residues within 4Å: Chain A: E.380, E.421 Ligands: ATP.2, MN.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.421 MN.10: 4 residues within 4Å: Chain B: E.414, E.421 Ligands: ATP.9, MN.12 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.414, B:E.421 MN.11: 2 residues within 4Å: Chain B: H.270 Ligands: ATP.9 No protein-ligand interaction detected (PLIP) MN.12: 4 residues within 4Å: Chain B: E.380, E.421 Ligands: ATP.9, MN.10 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.421

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 9 residues within 4Å: Chain A: L.190, R.194, I.257, N.258 Chain B: R.194, E.204, E.206, N.258 Ligands: GOL.13 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.194, A:R.194, A:N.258, B:R.194, B:N.258 Water bridges: A:R.259 GOL.7: 13 residues within 4Å: Chain A: P.214, G.215, A.217, S.218, A.219, P.221, I.237, K.446, D.451, E.452, A.453, M.454, F.455 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:P.214, A:A.217, A:A.219, A:K.446, A:F.455 Water bridges: A:K.446 GOL.13: 9 residues within 4Å: Chain A: R.194, E.204, E.206, N.258 Chain B: L.190, R.194, I.257, N.258 Ligands: GOL.6 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:R.194, A:E.206, A:N.258, B:R.194, B:R.194, B:N.258 Water bridges: A:E.204, A:E.204, B:R.259 GOL.14: 13 residues within 4Å: Chain B: P.214, G.215, A.217, S.218, A.219, P.221, I.237, K.446, D.451, E.452, A.453, M.454, F.455 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:P.214, B:A.217, B:A.219, B:K.446, B:F.455 Water bridges: B:K.446

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Desogus, G. et al., Active Site of Lysyl-tRNA Synthetase: Structural Studies of the Adenylation Reaction. Biochemistry (2000)

Release Date

2000-07-28

Peptides

LYSYL-TRNA SYNTHETASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

LYSYL-TRNA SYNTHETASE

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