SMTL ID : 9sfq.1

Structure at 1.9 A resolution of Thermus thermophilus tyrosyl-tRNA synthetase bound to wild-type tRNATyr(GUC).

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 7 residues within 4Å: Chain A: R.48, H.52, H.55, K.232, M.233, S.234, K.235 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:K.235 Water bridges: A:H.55, A:H.55, A:K.232, A:S.236 Salt bridges: A:R.48, A:H.52, A:H.55, A:K.232 SO4.2: 3 residues within 4Å: Chain A: T.39, K.71, R.187 6 PLIP interactions: 6 interactions with chain A Water bridges: A:T.39, A:E.124, A:I.186, A:R.187, A:R.187 Salt bridges: A:K.71 SO4.3: 6 residues within 4Å: Chain A: A.164, G.165 Chain B: G.79 Ligands: 1PE.10, PEG.17, PEG.18 No protein-ligand interaction detected (PLIP) SO4.20: 7 residues within 4Å: Chain C: R.48, H.52, H.55, K.232, M.233, S.234, K.235 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:K.235 Water bridges: C:H.55, C:H.55, C:K.232, C:S.236 Salt bridges: C:R.48, C:H.52, C:H.55, C:K.232 SO4.21: 3 residues within 4Å: Chain C: T.39, K.71, R.187 6 PLIP interactions: 6 interactions with chain C Water bridges: C:T.39, C:E.124, C:I.186, C:R.187, C:R.187 Salt bridges: C:K.71 SO4.22: 6 residues within 4Å: Chain C: A.164, G.165 Chain D: G.79 Ligands: 1PE.29, PEG.36, PEG.37 No protein-ligand interaction detected (PLIP)

20 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 1 residues within 4Å: Ligands: 1PE.9 Ligand excluded by PLIP PEG.5: 7 residues within 4Å: Chain A: R.142, L.143, S.145, L.146, A.210, Y.211 Chain C: P.86 Ligand excluded by PLIP PEG.6: 6 residues within 4Å: Chain A: K.16, A.19, E.20, E.21, I.22, E.25 Ligand excluded by PLIP PEG.7: 9 residues within 4Å: Chain A: V.225, G.229, R.230, P.258, D.259, P.260, L.261 Chain B: A.37, A.38 Ligand excluded by PLIP PEG.11: 7 residues within 4Å: Chain A: I.391, Q.392, R.394, V.402, L.403, T.404, P.406 Ligand excluded by PLIP PEG.12: 6 residues within 4Å: Chain A: G.43, A.44, D.45, R.48, D.196, Q.197 Ligand excluded by PLIP PEG.15: 7 residues within 4Å: Chain A: P.382, E.386, R.389 Chain B: C.10, U.45, G.46, G.47 Ligand excluded by PLIP PEG.16: 11 residues within 4Å: Chain B: G.1, C.82, A.83 Chain C: M.147, Q.151, F.199, L.202, V.203, E.206, R.209 Ligands: MG.13 Ligand excluded by PLIP PEG.17: 6 residues within 4Å: Chain B: C.4, A.5, G.79, C.80 Ligands: SO4.3, 1PE.10 Ligand excluded by PLIP PEG.18: 4 residues within 4Å: Chain B: G.6, G.7, U.78 Ligands: SO4.3 Ligand excluded by PLIP PEG.23: 1 residues within 4Å: Ligands: 1PE.28 Ligand excluded by PLIP PEG.24: 7 residues within 4Å: Chain A: P.86 Chain C: R.142, L.143, S.145, L.146, A.210, Y.211 Ligand excluded by PLIP PEG.25: 6 residues within 4Å: Chain C: K.16, A.19, E.20, E.21, I.22, E.25 Ligand excluded by PLIP PEG.26: 9 residues within 4Å: Chain C: V.225, G.229, R.230, P.258, D.259, P.260, L.261 Chain D: A.37, A.38 Ligand excluded by PLIP PEG.30: 7 residues within 4Å: Chain C: I.391, Q.392, R.394, V.402, L.403, T.404, P.406 Ligand excluded by PLIP PEG.31: 6 residues within 4Å: Chain C: G.43, A.44, D.45, R.48, D.196, Q.197 Ligand excluded by PLIP PEG.34: 7 residues within 4Å: Chain C: P.382, E.386, R.389 Chain D: C.10, U.45, G.46, G.47 Ligand excluded by PLIP PEG.35: 11 residues within 4Å: Chain A: M.147, Q.151, F.199, L.202, V.203, E.206, R.209 Chain D: G.1, C.82, A.83 Ligands: MG.32 Ligand excluded by PLIP PEG.36: 6 residues within 4Å: Chain D: C.4, A.5, G.79, C.80 Ligands: SO4.22, 1PE.29 Ligand excluded by PLIP PEG.37: 4 residues within 4Å: Chain D: G.6, G.7, U.78 Ligands: SO4.22 Ligand excluded by PLIP

8 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.8: 7 residues within 4Å: Chain A: L.223, V.225, G.229, R.230, L.261, S.264 Chain D: A.86 2 PLIP interactions: 2 interactions with chain A Water bridges: A:L.223, A:S.264 1PE.9: 8 residues within 4Å: Chain A: G.113, K.114, Q.118, E.119, P.120, P.303, Q.304 Ligands: PEG.4 3 PLIP interactions: 3 interactions with chain A Water bridges: A:G.113, A:Q.118, A:E.119 1PE.10: 9 residues within 4Å: Chain A: Y.162, E.163, A.164, G.165 Chain B: G.79, C.80 Ligands: SO4.3, PEG.17, 1PE.29 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.163 1PE.19: 7 residues within 4Å: Chain A: W.370, R.388, M.407, Q.409 Chain B: G.49, U.50, A.51 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.388 1PE.27: 7 residues within 4Å: Chain B: A.86 Chain C: L.223, V.225, G.229, R.230, L.261, S.264 2 PLIP interactions: 2 interactions with chain C Water bridges: C:L.223, C:S.264 1PE.28: 8 residues within 4Å: Chain C: G.113, K.114, Q.118, E.119, P.120, P.303, Q.304 Ligands: PEG.23 3 PLIP interactions: 3 interactions with chain C Water bridges: C:G.113, C:Q.118, C:E.119 1PE.29: 9 residues within 4Å: Chain C: Y.162, E.163, A.164, G.165 Chain D: G.79, C.80 Ligands: 1PE.10, SO4.22, PEG.36 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.163 1PE.38: 7 residues within 4Å: Chain C: W.370, R.388, M.407, Q.409 Chain D: G.49, U.50, A.51 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.388

4 x MG: MAGNESIUM ION(Non-functional Binders)

MG.13: 6 residues within 4Å: Chain B: G.1, G.2, C.81, C.82 Ligands: MG.14, PEG.16 No protein-ligand interaction detected (PLIP) MG.14: 1 residues within 4Å: Ligands: MG.13 No protein-ligand interaction detected (PLIP) MG.32: 6 residues within 4Å: Chain D: G.1, G.2, C.81, C.82 Ligands: MG.33, PEG.35 No protein-ligand interaction detected (PLIP) MG.33: 1 residues within 4Å: Ligands: MG.32 No protein-ligand interaction detected (PLIP)

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

2025-09-24

Peptides

Tyrosine--tRNA ligase: AC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

Tyrosine--tRNA ligase

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