SMTL ID : 7eiv.1

heterotetrameric glycyl-tRNA synthetase from Escherichia coli

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.68 Å

Oligo State

hetero-2-2-mer

Ligands

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

MG.1: 1 residues within 4Å: Ligands: ANP.3 No protein-ligand interaction detected (PLIP) MG.2: 4 residues within 4Å: Chain A: D.119, E.134, E.141 Ligands: ANP.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.141, A:E.141 MG.5: 4 residues within 4Å: Chain B: D.119, E.134, E.141 Ligands: ANP.7 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.141 MG.6: 1 residues within 4Å: Ligands: ANP.7 No protein-ligand interaction detected (PLIP)

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.3: 19 residues within 4Å: Chain A: R.64, D.67, N.75, R.76, L.77, Y.80, D.119, W.121, E.134, E.141, V.142, T.143, Q.144, T.164, G.166, R.169 Ligands: MG.1, MG.2, GLY.4 18 PLIP interactions: 17 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:R.64, A:R.64, A:D.67, A:D.67, A:R.76, A:R.76, A:L.77, A:D.119, A:E.141, A:E.141, A:T.143, A:G.166, A:R.169, A:R.169, G.4 pi-Stacking: A:Y.80, A:Y.80 pi-Cation interactions: A:R.169 ANP.7: 19 residues within 4Å: Chain B: R.64, D.67, N.75, R.76, L.77, Y.80, D.119, W.121, E.134, E.141, V.142, T.143, Q.144, T.164, G.166, R.169 Ligands: MG.5, MG.6, GLY.8 17 PLIP interactions: 16 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: B:R.64, B:R.64, B:D.67, B:R.76, B:R.76, B:L.77, B:D.119, B:E.141, B:E.141, B:T.143, B:G.166, B:R.169, B:R.169, G.8 pi-Stacking: B:Y.80, B:Y.80 pi-Cation interactions: B:R.169

2 x GLY: GLYCINE(Non-covalent)

GLY.4: 9 residues within 4Å: Chain A: A.37, T.39, R.64, Q.82, W.121, Q.144, E.162, T.164 Ligands: ANP.3 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.39, A:Q.82, A:E.162, A:T.164 Water bridges: A:T.39, A:T.39, A:R.64 Salt bridges: A:R.64 GLY.8: 9 residues within 4Å: Chain B: A.37, T.39, R.64, Q.82, W.121, Q.144, E.162, T.164 Ligands: ANP.7 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:T.39, B:Q.82, B:E.162, B:T.164 Water bridges: B:T.39, B:T.39 Salt bridges: B:R.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ju, Y. et al., X-shaped structure of bacterial heterotetrameric tRNA synthetase suggests cryptic prokaryote functions and a rationale for synthetase classifications. Nucleic Acids Res. (2021)

Release Date

2021-08-11

Peptides

Glycine--tRNA ligase alpha subunit: AB
Glycine--tRNA ligase beta subunit: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Glycine--tRNA ligase alpha subunit

Glycine--tRNA ligase beta subunit

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