SMTL ID : 7rou.1

Structure of human tyrosyl tRNA synthetase in complex with ML901-Tyr

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x 66I: {(2R,3S,4R,5R)-5-[4-amino-3-(difluoromethoxy)-1H-pyrazolo[3,4-d]pyrimidin-1-yl]-3,4-dihydroxyoxolan-2-yl}methyl [(2S)-2-amino-3-(4-hydroxyphenyl)propanoyl]sulfamate (non-preferred name)(Non-covalent)

66I.1: 24 residues within 4Å: Chain A: Y.40, W.41, G.42, T.43, A.44, H.50, Y.53, V.55, P.56, L.73, A.75, H.78, V.153, Y.167, Q.171, D.174, Q.183, G.185, G.186, D.188, Q.189, P.214, M.215, V.216 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:Y.40, A:L.73, A:A.75 Hydrogen bonds: A:Y.40, A:Y.40, A:G.42, A:A.44, A:Y.53, A:Y.167, A:Q.171, A:D.174, A:G.186, A:Q.189, A:V.216, A:V.216 Water bridges: A:Q.189 pi-Stacking: A:H.78 66I.9: 24 residues within 4Å: Chain B: Y.40, W.41, G.42, T.43, A.44, H.50, Y.53, V.55, P.56, L.73, A.75, H.78, V.153, Y.167, Q.171, D.174, Q.183, G.185, G.186, D.188, Q.189, P.214, M.215, V.216 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:Y.40, B:L.73, B:A.75 Hydrogen bonds: B:Y.40, B:Y.40, B:G.42, B:A.44, B:Y.53, B:Y.167, B:Q.171, B:D.174, B:G.186, B:Q.189, B:V.216, B:V.216 Water bridges: B:Q.189 pi-Stacking: B:H.78

14 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 2 residues within 4Å: Chain A: H.13, R.17 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.13, A:R.17 SO4.3: 2 residues within 4Å: Chain A: K.27, R.35 7 PLIP interactions: 7 interactions with chain A Water bridges: A:K.27, A:K.27, A:K.27, A:K.27, A:R.35 Salt bridges: A:K.27, A:R.35 SO4.4: 2 residues within 4Å: Chain A: K.283, W.284 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.284 Water bridges: A:D.281, A:K.283, A:K.283 Salt bridges: A:K.283 SO4.5: 4 residues within 4Å: Chain A: H.306, P.307, G.308, D.309 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.308, A:D.309 Water bridges: A:H.306, A:H.306 Salt bridges: A:H.306 SO4.6: 2 residues within 4Å: Chain A: S.127, K.128 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.128 Water bridges: A:E.129 SO4.7: 3 residues within 4Å: Chain A: R.17, K.65, P.271 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:P.271 Water bridges: A:R.17, A:R.17 Salt bridges: A:R.17, A:K.65 SO4.8: 1 residues within 4Å: Chain A: R.190 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.190, A:R.190 Salt bridges: A:R.190 SO4.10: 2 residues within 4Å: Chain B: H.13, R.17 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:H.13, B:R.17 SO4.11: 2 residues within 4Å: Chain B: K.27, R.35 7 PLIP interactions: 7 interactions with chain B Water bridges: B:K.27, B:K.27, B:K.27, B:K.27, B:R.35 Salt bridges: B:K.27, B:R.35 SO4.12: 2 residues within 4Å: Chain B: K.283, W.284 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:W.284 Water bridges: B:D.281, B:K.283, B:K.283 Salt bridges: B:K.283 SO4.13: 4 residues within 4Å: Chain B: H.306, P.307, G.308, D.309 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.308, B:D.309 Water bridges: B:H.306, B:H.306 Salt bridges: B:H.306 SO4.14: 2 residues within 4Å: Chain B: S.127, K.128 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.128 Water bridges: B:E.129 SO4.15: 3 residues within 4Å: Chain B: R.17, K.65, P.271 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:P.271 Water bridges: B:R.17, B:R.17 Salt bridges: B:R.17, B:K.65 SO4.16: 1 residues within 4Å: Chain B: R.190 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.190, B:R.190 Salt bridges: B:R.190

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xie, S.C. et al., Reaction hijacking of tyrosine tRNA synthetase as a new whole-of-life-cycle antimalarial strategy. Science (2022)

Release Date

2022-06-08

Peptides

Tyrosine--tRNA ligase, cytoplasmic: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Tyrosine--tRNA ligase, cytoplasmic