SMTL ID : 1q11.1

Crystal structure of an active fragment of human tyrosyl-tRNA synthetase with tyrosinol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

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

PO4.1: 4 residues within 4Å: Chain A: H.305, P.306, G.307, D.308 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.307, A:D.308 Water bridges: A:H.305, A:G.307, A:D.308 Salt bridges: A:H.305 PO4.6: 4 residues within 4Å: Chain B: H.305, P.306, G.307, D.308 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.307, B:D.308 Water bridges: B:H.305, B:G.307, B:D.308 Salt bridges: B:H.305

2 x K: POTASSIUM ION(Non-covalent)

K.2: 5 residues within 4Å: Chain A: T.42, A.43, T.45, Y.52, Y.97 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:A.43, A:Y.52, A:Y.97 K.7: 5 residues within 4Å: Chain B: T.42, A.43, T.45, Y.52, Y.97 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:A.43, B:Y.52, B:Y.97

2 x TYE: 4-[(2S)-2-amino-3-hydroxypropyl]phenol(Non-covalent)

TYE.3: 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 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.39, A:A.74 Hydrogen bonds: A:Y.39, A:Q.170, A:Q.170, A:D.173, A:D.173, A:Q.188 pi-Stacking: A:H.77 TYE.8: 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 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:Y.39, B:A.74 Hydrogen bonds: B:Y.39, B:Q.170, B:Q.170, B:D.173, B:D.173, B:Q.188 pi-Stacking: B:H.77

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 2 residues within 4Å: Chain A: H.12, R.16 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.16 GOL.5: 3 residues within 4Å: Chain A: S.126, K.127, E.128 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.127, A:E.128, A:E.128 GOL.9: 2 residues within 4Å: Chain B: H.12, R.16 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.16 GOL.10: 3 residues within 4Å: Chain B: S.126, K.127, E.128 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.127, B:E.128, B:E.128

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, X.-L. et al., Crystal structures that suggest late development of genetic code components for differentiating aromatic side chains. Proc.Natl.Acad.Sci.USA (2003)

Release Date

2004-01-06

Peptides

Tyrosyl-tRNA synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Tyrosyl-tRNA synthetase

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