SMTL ID : 4q93.1

Crystal structure of resveratrol bound human tyrosyl tRNA synthetase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x STL: RESVERATROL(Non-covalent)

STL.1: 10 residues within 4Å: Chain A: Y.39, G.41, A.43, L.72, A.74, H.77, Y.166, Q.170, D.173, Q.182 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.39, A:L.72, A:A.74, A:Y.166, A:Q.170 Hydrogen bonds: A:Y.39, A:Y.166, A:D.173, A:D.173 Water bridges: A:Q.170, A:Q.170 pi-Stacking: A:H.77 STL.13: 10 residues within 4Å: Chain B: Y.39, G.41, A.43, L.72, A.74, H.77, Y.166, Q.170, D.173, Q.182 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:Y.39, B:L.72, B:A.74, B:Y.166, B:Q.170 Hydrogen bonds: B:Y.39, B:Y.166, B:D.173, B:D.173 Water bridges: B:Q.170, B:Q.170 pi-Stacking: B:H.77

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

SO4.2: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.12 SO4.3: 2 residues within 4Å: Chain A: K.26, R.34 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.26, A:R.34 SO4.4: 4 residues within 4Å: Chain A: H.305, P.306, G.307, D.308 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.307, A:D.308 Salt bridges: A:H.305 SO4.5: 3 residues within 4Å: Chain A: H.12, R.16, S.273 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.12, A:R.16 SO4.6: 2 residues within 4Å: Chain A: D.280, E.281 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.281 SO4.7: 6 residues within 4Å: Chain A: V.50, A.51, G.217, L.218, T.219, K.231 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.51, A:L.218, A:T.219 SO4.14: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain B Water bridges: B:H.12 SO4.15: 2 residues within 4Å: Chain B: K.26, R.34 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.26, B:R.34 SO4.16: 4 residues within 4Å: Chain B: H.305, P.306, G.307, D.308 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.307, B:D.308 Salt bridges: B:H.305 SO4.17: 3 residues within 4Å: Chain B: H.12, R.16, S.273 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:H.12, B:R.16 SO4.18: 2 residues within 4Å: Chain B: D.280, E.281 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.281 SO4.19: 6 residues within 4Å: Chain B: V.50, A.51, G.217, L.218, T.219, K.231 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.51, B:L.218, B:T.219

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.8: 2 residues within 4Å: Chain A: K.265, H.266 Ligand excluded by PLIP CL.20: 2 residues within 4Å: Chain B: K.265, H.266 Ligand excluded by PLIP

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 3 residues within 4Å: Chain A: S.126, K.127, E.128 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.127, A:E.128, A:E.128 Water bridges: A:L.125, B:K.127 GOL.10: 1 residues within 4Å: Chain A: E.151 No protein-ligand interaction detected (PLIP) GOL.21: 3 residues within 4Å: Chain B: S.126, K.127, E.128 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.127, B:E.128, B:E.128 Water bridges: A:K.127, A:K.127 GOL.22: 1 residues within 4Å: Chain B: E.151 No protein-ligand interaction detected (PLIP)

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.11: 1 residues within 4Å: Chain A: R.189 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.189 PO4.12: 1 residues within 4Å: Chain A: K.265 5 PLIP interactions: 5 interactions with chain A Water bridges: A:N.17, A:L.18, A:K.265, A:K.265 Salt bridges: A:K.265 PO4.23: 1 residues within 4Å: Chain B: R.189 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.189 PO4.24: 1 residues within 4Å: Chain B: K.265 5 PLIP interactions: 5 interactions with chain B Water bridges: B:N.17, B:L.18, B:K.265, B:K.265 Salt bridges: B:K.265

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sajish, M. et al., A human tRNA synthetase is a potent PARP1-activating effector target for resveratrol. Nature (2014)

Release Date

2014-12-17

Peptides

Tyrosine--tRNA ligase, cytoplasmic: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Tyrosine--tRNA ligase, cytoplasmic

Related Entries With Identical Sequence