SMTL ID : 6m0t.1 (1 other biounit)

Crystal Structure of Lysyl-tRNA Synthetase from Plasmodium falciparum complexed with L-lysine and Cladosporin derivative (CL-2)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.68 Å

Oligo State

homo-dimer

Ligands

2 x LYS: LYSINE(Non-covalent)

LYS.1: 13 residues within 4Å: Chain A: G.208, A.230, E.232, R.254, E.270, Y.272, N.427, Y.429, E.431, G.476, L.477, G.478 Ligands: EZ3.2 7 PLIP interactions: 6 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:G.208, A:E.270, A:E.270, A:E.270, A:N.427, K.1 Salt bridges: A:R.254 LYS.3: 14 residues within 4Å: Chain B: G.208, A.209, A.230, E.232, R.254, E.270, Y.272, N.427, Y.429, E.431, G.476, L.477, G.478 Ligands: EZ3.4 8 PLIP interactions: 8 interactions with chain B, Hydrophobic interactions: B:E.270, B:Y.429 Hydrogen bonds: B:G.208, B:E.232, B:Y.272, B:N.427, B:E.431 Salt bridges: B:R.254

2 x EZ3: (3R)-3-[(R)-[(2R,6S)-6-methyloxan-2-yl]-oxidanyl-methyl]-6,8-bis(oxidanyl)-3,4-dihydroisochromen-1-one(Non-covalent)

EZ3.2: 15 residues within 4Å: Chain A: R.254, T.261, H.262, N.263, F.266, S.268, E.424, V.425, L.426, N.427, G.478, G.480, R.483, I.494 Ligands: LYS.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:H.262, A:E.424, A:N.427 Hydrogen bonds: A:N.263, A:N.263 Water bridges: A:D.482, A:R.483 Salt bridges: A:R.483 pi-Stacking: A:H.262, A:F.266 EZ3.4: 15 residues within 4Å: Chain B: R.254, E.256, T.261, H.262, N.263, F.266, E.424, V.425, L.426, N.427, G.478, G.480, R.483, I.494 Ligands: LYS.3 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:H.262, B:N.427 Hydrogen bonds: B:E.256, B:E.256, B:N.263, B:N.263 Salt bridges: B:R.483 pi-Stacking: B:H.262, B:F.266

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Babbar, P. et al., Design, Synthesis, and Structural Analysis of Cladosporin-Based Inhibitors of Malaria Parasites. Acs Infect Dis. (2021)

Release Date

2021-04-21

Peptides

Lysine--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Lysine--tRNA ligase

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