SMTL ID : 9sfb.1

Structure at 2.7 A resolution of Thermus thermophilus tyrosyl-tRNA synthetase bound to a tRNA(Tyr)(GUA) transcript, the sulphamoyl analogue of tyrosyl-adenylate and pyrophosphate.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

monomer

Ligands

1 x PPV: PYROPHOSPHATE(Non-covalent)

PPV.1: 9 residues within 4Å: Chain A: T.47, H.52, H.55, R.93, M.233, S.234, K.235, S.236 Ligands: YSA.8 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.47, A:K.235, A:S.236 Salt bridges: A:H.52, A:H.55, A:R.93, A:K.232

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

SO4.2: 3 residues within 4Å: Chain A: R.48, P.49, K.235 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.48 Salt bridges: A:K.235 SO4.3: 5 residues within 4Å: Chain A: L.398, Q.409, V.410, D.411, R.416 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.411 Salt bridges: A:R.416 SO4.4: 3 residues within 4Å: Chain A: R.48, R.89, P.94 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.48, A:R.89 SO4.5: 1 residues within 4Å: Chain A: R.117 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.117 SO4.6: 5 residues within 4Å: Chain A: S.87, G.88, R.155, E.156, D.157 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.88, A:E.156, A:D.157 Salt bridges: A:R.155 SO4.7: 2 residues within 4Å: Chain A: R.102, E.133 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.102

1 x YSA: 5'-O-[N-(L-TYROSYL)SULFAMOYL]ADENOSINE(Non-covalent)

YSA.8: 28 residues within 4Å: Chain A: K.41, L.42, G.43, A.44, D.45, H.52, G.54, H.55, V.57, V.58, T.80, D.85, N.128, Y.175, Q.179, D.182, E.191, G.193, G.194, D.196, Q.197, N.200, P.222, L.223, L.224, K.232, M.233 Ligands: PPV.1 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Q.179 Hydrogen bonds: A:K.41, A:D.45, A:D.85, A:Q.179, A:Q.179, A:D.182, A:G.194, A:D.196, A:Q.197, A:N.200, A:L.224, A:M.233, A:M.233

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yaremchuk, A. et al., Class I tyrosyl-tRNA synthetase has a class II mode of cognate tRNA recognition. EMBO J (2002)

Release Date

2025-09-03

Peptides

Tyrosine--tRNA ligase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Tyrosine--tRNA ligase

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