SMTL ID : 5eln.1 (1 other biounit)

Crystal Structure of Lysyl-tRNA Synthetase from Cryptosporidium parvum complexed with L-lysine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x LYS: LYSINE(Non-covalent)

LYS.1: 13 residues within 4Å: Chain A: G.225, A.226, A.247, E.249, E.287, Y.289, N.443, A.444, Y.445, E.447, G.492, W.493, G.494 7 PLIP interactions: 7 interactions with chain A, Hydrophobic interactions: A:Y.445 Hydrogen bonds: A:G.225, A:E.249, A:E.287, A:Y.289, A:N.443, A:E.447 LYS.5: 13 residues within 4Å: Chain B: G.225, A.226, A.247, E.249, R.271, E.287, Y.289, N.443, Y.445, E.447, G.492, W.493, G.494 6 PLIP interactions: 6 interactions with chain B, Hydrophobic interactions: B:Y.445 Hydrogen bonds: B:G.225, B:E.287, B:N.443, B:E.447 Salt bridges: B:R.271

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 7 residues within 4Å: Chain A: I.199, R.203, I.266 Chain B: R.203, E.213, E.215 Ligands: EDO.6 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.203, B:E.213, A:R.203, A:R.203, A:I.266 EDO.3: 3 residues within 4Å: Chain A: G.328, K.329, C.330 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.328, A:C.330, A:C.330 EDO.4: 6 residues within 4Å: Chain A: W.421, H.422, R.423, E.424, K.425, P.426 3 PLIP interactions: 3 interactions with chain A Water bridges: A:W.421, A:R.423, A:R.423 EDO.6: 7 residues within 4Å: Chain A: R.203, E.213, E.215 Chain B: I.199, R.203, I.266 Ligands: EDO.2 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.203, B:R.203, B:I.266, A:R.203 Water bridges: A:E.213, A:E.213 EDO.7: 8 residues within 4Å: Chain A: M.218, I.266, G.267, K.268 Chain B: M.218, I.266, G.267, K.268 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.268, A:K.268 EDO.8: 7 residues within 4Å: Chain B: N.220, I.222, Y.223, G.224, R.245, L.250, Y.251 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.220, B:I.222 Water bridges: B:G.224, B:G.224, B:G.224

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Baragana, B. et al., Lysyl-tRNA synthetase as a drug target in malaria and cryptosporidiosis. Proc. Natl. Acad. Sci. U.S.A. (2019)

Release Date

2016-11-16

Peptides

Lysine--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Lysine--tRNA ligase

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