SMTL ID : 9sdf.1

Structure at 1.9 A resolution of Thermus thermophilus tyrosyl-tRNA synthetase bound to wild-type modified tRNA(Tyr), tyrosine and AMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 19 residues within 4Å: Chain A: L.42, G.43, A.44, D.45, H.52, G.54, H.55, V.57, V.58, G.193, G.194, D.196, Q.197, P.222, L.223, L.224, K.232, M.233 Ligands: TYR.2 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.194, A:D.196, A:L.224, A:M.233, A:M.233 Water bridges: A:D.45, A:H.52, A:H.55, A:H.55 Salt bridges: A:H.55 AMP.17: 19 residues within 4Å: Chain C: L.42, G.43, A.44, D.45, H.52, G.54, H.55, V.57, V.58, G.193, G.194, D.196, Q.197, P.222, L.223, L.224, K.232, M.233 Ligands: TYR.18 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:G.194, C:D.196, C:L.224, C:M.233, C:M.233 Water bridges: C:D.45, C:H.52, C:H.55, C:H.55 Salt bridges: C:H.55

2 x TYR: TYROSINE(Non-covalent)

TYR.2: 16 residues within 4Å: Chain A: K.41, G.43, A.44, D.45, I.75, G.77, T.80, D.85, N.128, Y.175, Q.179, D.182, E.191, Q.197, N.200 Ligands: AMP.1 8 PLIP interactions: 7 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:Q.179 Hydrogen bonds: A:K.41, A:D.45, A:D.85, A:Y.175, A:D.182, A:Q.197, Y.2 TYR.18: 16 residues within 4Å: Chain C: K.41, G.43, A.44, D.45, I.75, G.77, T.80, D.85, N.128, Y.175, Q.179, D.182, E.191, Q.197, N.200 Ligands: AMP.17 10 PLIP interactions: 9 interactions with chain C, 1 Ligand-Ligand interactions Hydrophobic interactions: C:Q.179 Hydrogen bonds: C:K.41, C:D.45, C:D.85, C:D.85, C:Y.175, C:D.182, C:D.182, C:Q.197, Y.18

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

PEG.3: 5 residues within 4Å: Chain A: S.362, E.363, L.364, K.365, R.373 No protein-ligand interaction detected (PLIP) PEG.8: 6 residues within 4Å: Chain A: A.164, G.165, I.166 Chain B: G.13, G.79 Ligands: PGE.9 No protein-ligand interaction detected (PLIP) PEG.12: 7 residues within 4Å: Chain A: P.382, E.386, R.389 Chain B: C.10, U.45, G.46, G.47 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.389 PEG.13: 6 residues within 4Å: Chain B: G.3, C.4, A.5, G.79, C.80, C.81 No protein-ligand interaction detected (PLIP) PEG.14: 7 residues within 4Å: Chain C: M.147, Q.151, F.199, L.202, V.203, E.206, R.209 2 PLIP interactions: 2 interactions with chain C Water bridges: C:Q.151, C:R.209 PEG.19: 5 residues within 4Å: Chain C: S.362, E.363, L.364, K.365, R.373 No protein-ligand interaction detected (PLIP) PEG.24: 6 residues within 4Å: Chain C: A.164, G.165, I.166 Chain D: G.13, G.79 Ligands: PGE.25 No protein-ligand interaction detected (PLIP) PEG.28: 7 residues within 4Å: Chain C: P.382, E.386, R.389 Chain D: C.10, U.45, G.46, G.47 1 PLIP interactions: 1 interactions with chain C Water bridges: C:R.389 PEG.29: 6 residues within 4Å: Chain D: G.3, C.4, A.5, G.79, C.80, C.81 No protein-ligand interaction detected (PLIP) PEG.30: 7 residues within 4Å: Chain A: M.147, Q.151, F.199, L.202, V.203, E.206, R.209 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.151, A:R.209

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

SO4.4: 4 residues within 4Å: Chain A: L.227, K.252, K.253, R.256 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.256 SO4.15: 4 residues within 4Å: Chain B: C.29, A.39, C.41, C.42 No protein-ligand interaction detected (PLIP) SO4.20: 4 residues within 4Å: Chain C: L.227, K.252, K.253, R.256 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.256 SO4.31: 4 residues within 4Å: Chain D: C.29, A.39, C.41, C.42 No protein-ligand interaction detected (PLIP)

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

1PE.5: 6 residues within 4Å: Chain A: V.225, G.229, R.230, P.260, L.261, S.264 2 PLIP interactions: 2 interactions with chain A Water bridges: A:L.223, A:V.225 1PE.6: 8 residues within 4Å: Chain A: A.110, G.113, K.114, Q.118, E.119, P.120, P.303, Q.304 No protein-ligand interaction detected (PLIP) 1PE.7: 9 residues within 4Å: Chain A: K.31, R.36, R.187, A.188, D.189, Q.208, G.212, Q.213, S.214 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.187 Water bridges: A:R.36, A:Q.213, A:S.214, A:S.214 1PE.10: 6 residues within 4Å: Chain A: K.16, A.19, E.20, E.21, I.22, E.25 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.16 Water bridges: A:I.22 1PE.16: 7 residues within 4Å: Chain A: W.370, R.388, M.407, Q.409 Chain B: G.49, U.50, A.51 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.388, A:R.388 1PE.21: 6 residues within 4Å: Chain C: V.225, G.229, R.230, P.260, L.261, S.264 2 PLIP interactions: 2 interactions with chain C Water bridges: C:L.223, C:V.225 1PE.22: 8 residues within 4Å: Chain C: A.110, G.113, K.114, Q.118, E.119, P.120, P.303, Q.304 No protein-ligand interaction detected (PLIP) 1PE.23: 9 residues within 4Å: Chain C: K.31, R.36, R.187, A.188, D.189, Q.208, G.212, Q.213, S.214 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.187 Water bridges: C:R.36, C:Q.213, C:S.214, C:S.214 1PE.26: 6 residues within 4Å: Chain C: K.16, A.19, E.20, E.21, I.22, E.25 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.16 Water bridges: C:I.22 1PE.32: 7 residues within 4Å: Chain C: W.370, R.388, M.407, Q.409 Chain D: G.49, U.50, A.51 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.388, C:R.388

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.9: 8 residues within 4Å: Chain A: Y.162, E.163, A.164, G.165 Chain B: G.79, C.80 Ligands: PEG.8, PGE.25 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Y.162, A:Y.162 PGE.25: 8 residues within 4Å: Chain C: Y.162, E.163, A.164, G.165 Chain D: G.79, C.80 Ligands: PGE.9, PEG.24 2 PLIP interactions: 2 interactions with chain C Water bridges: C:Y.162, C:Y.162

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

MG.11: 4 residues within 4Å: Chain B: G.1, G.2, C.81, C.82 No protein-ligand interaction detected (PLIP) MG.27: 4 residues within 4Å: Chain D: G.1, G.2, C.81, C.82 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

2025-09-03

Peptides

Tyrosine--tRNA ligase: AC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

Tyrosine--tRNA ligase

Related Entries With Identical Sequence