SMTL ID : 5fog.4 (3 other biounits)

Crystal structure of hte Cryptosporidium muris cytosolic leucyl-tRNA synthetase editing domain complex with a post-transfer editing analogue of norvaline (Nv2AA)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x VRT: 2'-(L-NORVALYL)AMINO-2'-DEOXYADENOSINE(Non-covalent)

VRT.1: 18 residues within 4Å: Chain A: Y.9, A.37, T.38, L.39, R.40, T.43, M.44, I.165, S.166, K.169, G.170, G.172, V.174, T.175, V.177, S.181, D.184, K.247 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:T.43, A:V.177, A:V.177 Hydrogen bonds: A:Y.9, A:T.38, A:T.38, A:L.39, A:S.166, A:S.166, A:G.172, A:S.181, A:S.181, A:K.247 Water bridges: A:R.40 VRT.3: 16 residues within 4Å: Chain B: Y.9, A.37, T.38, L.39, R.40, T.43, I.165, S.166, K.169, G.172, V.174, T.175, V.177, S.181, D.184, K.247 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:T.43, B:V.177 Hydrogen bonds: B:T.38, B:L.39, B:S.166, B:S.166, B:K.169, B:G.172, B:S.181, B:S.181, B:K.247 Water bridges: B:T.171, B:T.175, B:K.247

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

EDO.2: 3 residues within 4Å: Chain A: Y.256, K.269, C.271 No protein-ligand interaction detected (PLIP) EDO.4: 4 residues within 4Å: Chain B: L.212, E.213, R.262 Ligands: EDO.5 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.213, B:R.262 EDO.5: 4 residues within 4Å: Chain B: Y.45, P.153, R.262 Ligands: EDO.4 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.45

1 x K: POTASSIUM ION(Non-covalent)

K.6: 3 residues within 4Å: Chain B: A.149, T.152, Y.154 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:A.149, B:T.152, H2O.6, H2O.6

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Palencia, A. et al., Cryptosporidium and Toxoplasma Parasites are Inhibited by a Benzoxaborole Targeting Leucyl-tRNA Synthetase. Antimicrob.Agents Chemother. (2016)

Release Date

2016-08-03

Peptides

LEUCYL-TRNA SYNTHETASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

LEUCYL-TRNA SYNTHETASE

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