SMTL ID : 1e1o.1

lysyl-tRNA Synthetase (LYSU) hexagonal form, complexed with lysine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.12 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, M.276, E.278, Y.280, N.424, F.426, E.428, G.473, G.475 12 PLIP interactions: 12 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, A:R.262, A:R.262, A:R.262 Salt bridges: A:R.262 LYS.10: 13 residues within 4Å: Chain B: G.216, A.217, A.238, E.240, R.262, M.276, E.278, Y.280, N.424, F.426, E.428, G.473, G.475 9 PLIP interactions: 9 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, B:R.262, B:R.262, B:R.262 Salt bridges: B:R.262

16 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 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.11 Ligand excluded by PLIP GOL.3: 8 residues within 4Å: Chain A: Y.286, T.390, E.391, N.403, I.409, T.410, D.411, R.412 Ligand excluded by PLIP GOL.4: 3 residues within 4Å: Chain A: A.381, H.382, I.384 Ligand excluded by PLIP GOL.5: 7 residues within 4Å: Chain A: A.217, S.218, V.396, R.412, N.424, F.426, M.454 Ligand excluded by PLIP GOL.6: 3 residues within 4Å: Chain A: H.315, I.384, Q.385 Ligand excluded by PLIP GOL.7: 5 residues within 4Å: Chain A: H.270, N.271, F.274, R.480, I.491 Ligand excluded by PLIP GOL.8: 12 residues within 4Å: Chain A: P.214, G.215, A.217, S.218, A.219, P.221, I.237, D.451, E.452, A.453, M.454, F.455 Ligand excluded by PLIP GOL.9: 1 residues within 4Å: Chain A: K.333 Ligand excluded by PLIP GOL.11: 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.2 Ligand excluded by PLIP GOL.12: 8 residues within 4Å: Chain B: Y.286, T.390, E.391, N.403, I.409, T.410, D.411, R.412 Ligand excluded by PLIP GOL.13: 3 residues within 4Å: Chain B: A.381, H.382, I.384 Ligand excluded by PLIP GOL.14: 7 residues within 4Å: Chain B: A.217, S.218, V.396, R.412, N.424, F.426, M.454 Ligand excluded by PLIP GOL.15: 3 residues within 4Å: Chain B: H.315, I.384, Q.385 Ligand excluded by PLIP GOL.16: 5 residues within 4Å: Chain B: H.270, N.271, F.274, R.480, I.491 Ligand excluded by PLIP GOL.17: 12 residues within 4Å: Chain B: P.214, G.215, A.217, S.218, A.219, P.221, I.237, D.451, E.452, A.453, M.454, F.455 Ligand excluded by PLIP GOL.18: 1 residues within 4Å: Chain B: K.333 Ligand excluded by PLIP

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, HEAT INDUCIBLE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

LYSYL-TRNA SYNTHETASE, HEAT INDUCIBLE

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