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

Crystal structure of PfKRS complexed with chromone inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

2 x 9X0: N-(cyclohexylmethyl)-4-oxo-4H-1-benzopyran-2-carboxamide(Non-covalent)

9X0.1: 16 residues within 4Å: Chain A: R.254, E.256, T.261, H.262, N.263, F.266, E.424, V.425, L.426, N.427, G.478, L.479, G.480, R.483, I.494 Ligands: LYS.7 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:R.254, A:E.256, A:H.262, A:F.266, A:F.266, A:N.427 Hydrogen bonds: A:N.263 Water bridges: A:R.483, A:R.483 pi-Stacking: A:H.262, A:F.266 9X0.8: 16 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, L.479, G.480, R.483, I.494 Ligands: LYS.10 14 PLIP interactions: 13 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:R.254, B:E.256, B:H.262, B:F.266, B:F.266, B:F.266, B:N.427, K.10 Hydrogen bonds: B:N.263 Water bridges: B:R.254, B:E.424, B:R.483 pi-Stacking: B:H.262, B:F.266

2 x CO: COBALT (II) ION(Non-covalent)

CO.2: 1 residues within 4Å: Chain A: D.374 No protein-ligand interaction detected (PLIP) CO.9: 1 residues within 4Å: Chain B: D.374 No protein-ligand interaction detected (PLIP)

3 x FMT: FORMIC ACID(Non-functional Binders)

FMT.3: 5 residues within 4Å: Chain A: I.182, R.186, I.249 Chain B: R.186, E.196 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.186, A:R.186, A:I.249, B:R.186 FMT.4: 1 residues within 4Å: Chain A: R.192 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.192 Water bridges: A:D.287, A:D.287 FMT.5: 5 residues within 4Å: Chain A: R.186, E.196 Chain B: I.182, R.186, I.249 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.186, B:R.186, A:R.186, A:E.196

1 x MLA: MALONIC ACID(Non-covalent)

MLA.6: 8 residues within 4Å: Chain A: K.245, W.273, A.274, Y.275, A.276 Chain B: K.29, E.31, R.32 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Water bridges: B:E.31, B:E.31, B:R.32, B:R.32, B:R.32 Salt bridges: B:K.29, B:R.32, A:K.245 Hydrogen bonds: A:A.274

2 x LYS: LYSINE(Non-covalent)

LYS.7: 14 residues within 4Å: Chain A: 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: 9X0.1 9 PLIP interactions: 8 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:Y.429 Hydrogen bonds: A:G.208, A:G.208, A:E.232, A:N.427, A:E.431, K.7 Water bridges: A:R.254 Salt bridges: A:R.254 LYS.10: 15 residues within 4Å: Chain B: G.208, A.209, A.230, E.232, R.254, E.270, Y.272, N.427, A.428, Y.429, E.431, G.476, L.477, G.478 Ligands: 9X0.8 11 PLIP interactions: 10 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:Y.429 Hydrogen bonds: B:G.208, B:E.232, B:E.270, B:N.427, B:E.431, K.10 Water bridges: B:T.231, B:R.254, B:R.254 Salt bridges: B:R.254

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

2019-03-13

Peptides

Lysine--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Lysine--tRNA ligase

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