SMTL ID : 6n67.1

Crystal structure of the ligase domain of fungal tRNA ligase Trl1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x APC: DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER(Non-covalent)

APC.1: 17 residues within 4Å: Chain A: R.119, Y.138, K.140, F.141, T.166, L.167, K.168, E.169, I.173, K.189, E.238, H.261, T.290, V.323, R.325, K.343, K.345 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:R.119, A:T.166, A:L.167, A:K.168, A:E.169, A:R.325, A:K.345, A:K.345 Water bridges: A:K.343, A:K.345 Salt bridges: A:R.119, A:K.189 pi-Stacking: A:H.261, A:H.261

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

SO4.2: 5 residues within 4Å: Chain A: N.170, H.247, I.248, R.354, R.357 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.170 Salt bridges: A:H.247, A:R.354, A:R.357 SO4.3: 4 residues within 4Å: Chain A: T.50, A.51, R.231, L.277 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.51 Salt bridges: A:R.231

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 2 residues within 4Å: Chain A: C.172, I.173 Ligand excluded by PLIP CL.5: 1 residues within 4Å: Chain A: R.229 Ligand excluded by PLIP CL.6: 1 residues within 4Å: Chain A: Y.53 Ligand excluded by PLIP

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 6 residues within 4Å: Chain A: S.188, S.191, R.195, S.201, H.202, S.203 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.188, A:R.195, A:R.195, A:H.202, A:S.203, A:S.203 GOL.8: 3 residues within 4Å: Chain A: T.220, K.221, E.222 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.221, A:E.222 GOL.9: 7 residues within 4Å: Chain A: Y.53, S.55, Q.56, E.132, R.229, K.230, N.232 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.56, A:Q.56, A:E.132, A:R.229, A:N.232 GOL.10: 5 residues within 4Å: Chain A: E.246, L.398, H.403, G.404, K.407 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.404 Water bridges: A:H.403, A:K.407

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Peschek, J. et al., tRNA ligase structure reveals kinetic competition between non-conventional mRNA splicing and mRNA decay. Elife (2019)

Release Date

2019-07-03

Peptides

tRNA ligase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

tRNA ligase