SMTL ID : 4j75.1

Crystal Structure of a parasite tRNA synthetase, product-bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x TYM: TRYPTOPHANYL-5'AMP(Non-covalent)

TYM.1: 24 residues within 4Å: Chain A: Y.83, T.84, G.85, R.86, G.87, G.96, H.97, P.100, Q.118, S.120, E.123, K.124, Y.202, Q.206, Q.229, G.230, D.232, Q.233, F.237, V.258, F.259, M.260, K.269, M.270 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:Y.83, A:Q.233, A:F.237, A:F.237 Hydrogen bonds: A:Y.83, A:G.87, A:Q.206, A:Q.206, A:G.230, A:D.232, A:Q.233, A:M.260, A:M.260, A:M.270 Water bridges: A:G.85, A:K.124, A:K.124, A:K.124, A:K.269 Salt bridges: A:R.86, A:K.124 pi-Stacking: A:F.259 TYM.4: 27 residues within 4Å: Chain B: Y.83, T.84, G.85, R.86, G.87, H.94, G.96, H.97, P.100, Q.118, S.120, E.123, K.124, Y.202, Q.206, V.227, P.228, Q.229, G.230, D.232, Q.233, F.237, V.258, F.259, M.260, K.269, M.270 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:Y.83, B:V.227, B:Q.229, B:Q.233, B:F.237, B:F.237 Hydrogen bonds: B:Y.83, B:G.87, B:S.120, B:Q.206, B:Q.206, B:G.230, B:D.232, B:Q.233, B:M.260, B:M.270, B:M.270 Water bridges: B:T.84 Salt bridges: B:R.86, B:H.97, B:K.124 pi-Stacking: B:F.259

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: N.141, K.161, E.164 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.161, A:K.161 Water bridges: A:N.141 GOL.3: 7 residues within 4Å: Chain A: H.53, H.54, Y.102, Y.340, L.341, E.343, L.376 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.53, A:H.54

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koh, C.Y. et al., Crystal structures of Plasmodium falciparum cytosolic tryptophanyl-tRNA synthetase and its potential as a target for structure-guided drug design. Mol.Biochem.Parasitol. (2013)

Release Date

2013-05-22

Peptides

Tryptophanyl-tRNA synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Tryptophanyl-tRNA synthetase

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