SMTL ID : 4qbt.1

Crystal structure of tyrosine bound human tyrosyl tRNA synthetase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

PO4.1: 4 residues within 4Å: Chain A: H.305, P.306, G.307, D.308 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.307, A:D.308 Water bridges: A:H.305 Salt bridges: A:H.305 PO4.7: 2 residues within 4Å: Chain A: K.282, W.283 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.282, A:K.282 Salt bridges: A:K.282 PO4.8: 8 residues within 4Å: Chain A: H.49, V.50, A.51, G.217, L.218, T.219, K.231, I.232 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:V.50, A:A.51, A:L.218, A:T.219, A:I.232 Salt bridges: A:H.49 PO4.10: 4 residues within 4Å: Chain B: H.305, P.306, G.307, D.308 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.307, B:D.308 Water bridges: B:H.305 Salt bridges: B:H.305 PO4.16: 2 residues within 4Å: Chain B: K.282, W.283 3 PLIP interactions: 3 interactions with chain B Water bridges: B:K.282, B:K.282 Salt bridges: B:K.282 PO4.17: 8 residues within 4Å: Chain B: H.49, V.50, A.51, G.217, L.218, T.219, K.231, I.232 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:V.50, B:A.51, B:L.218, B:T.219, B:I.232 Salt bridges: B:H.49

4 x K: POTASSIUM ION(Non-covalent)

K.2: 6 residues within 4Å: Chain A: T.42, A.43, T.45, Y.52, Y.97 Ligands: K.9 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:A.43, A:Y.52, H2O.1 K.9: 3 residues within 4Å: Chain A: T.45, K.84 Ligands: K.2 No protein-ligand interaction detected (PLIP) K.11: 6 residues within 4Å: Chain B: T.42, A.43, T.45, Y.52, Y.97 Ligands: K.18 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:A.43, B:Y.52, H2O.7 K.18: 3 residues within 4Å: Chain B: T.45, K.84 Ligands: K.11 No protein-ligand interaction detected (PLIP)

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 2 residues within 4Å: Chain A: H.12, R.16 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.16 GOL.4: 3 residues within 4Å: Chain A: S.126, K.127, E.128 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.127, A:E.128 GOL.12: 2 residues within 4Å: Chain B: H.12, R.16 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.16 GOL.13: 3 residues within 4Å: Chain B: S.126, K.127, E.128 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.127, B:E.128

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

SO4.5: 2 residues within 4Å: Chain A: K.26, R.34 4 PLIP interactions: 4 interactions with chain A Water bridges: A:D.180, A:D.180 Salt bridges: A:K.26, A:R.34 SO4.14: 2 residues within 4Å: Chain B: K.26, R.34 4 PLIP interactions: 4 interactions with chain B Water bridges: B:D.180, B:D.180 Salt bridges: B:K.26, B:R.34

2 x TYR: TYROSINE(Non-covalent)

TYR.6: 12 residues within 4Å: Chain A: Y.39, G.41, A.43, L.72, A.74, H.77, V.152, Y.166, Q.170, D.173, Q.182, Q.188 13 PLIP interactions: 12 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:Y.39, A:A.74 Hydrogen bonds: A:Y.39, A:Y.39, A:Y.166, A:Q.170, A:Q.170, A:D.173, A:Q.188, Y.6 Water bridges: A:A.43, A:A.43 pi-Stacking: A:H.77 TYR.15: 12 residues within 4Å: Chain B: Y.39, G.41, A.43, L.72, A.74, H.77, V.152, Y.166, Q.170, D.173, Q.182, Q.188 13 PLIP interactions: 12 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:Y.39, B:A.74 Hydrogen bonds: B:Y.39, B:Y.39, B:Y.166, B:Q.170, B:Q.170, B:D.173, B:Q.188, Y.15 Water bridges: B:A.43, B:A.43 pi-Stacking: B:H.77

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

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