SMTL ID : 7yse.1

Crystal structure of E. coli heterotetrameric GlyRS in complex with tRNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.91 Å

Oligo State

hetero-2-2-mer

Ligands

2 x JPO: [(2R,3S,4R,5R)-5-(6-azanyl-2-chloranyl-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl N-(2-azanylethanoyl)sulfamate(Non-covalent)

JPO.1: 19 residues within 4Å: Chain A: A.37, T.39, R.64, D.67, N.75, R.76, L.77, Y.80, Q.82, W.121, E.141, V.142, T.143, Q.144, E.162, T.164, G.166, R.169 Chain E: A.76 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:T.39, A:R.64, A:R.64, A:D.67, A:L.77, A:L.77, A:Q.82, A:T.143, A:E.162, A:T.164, A:G.166, A:R.169 Salt bridges: A:R.64 pi-Stacking: A:Y.80, A:Y.80 JPO.3: 20 residues within 4Å: Chain B: A.37, T.39, R.64, D.67, N.75, R.76, L.77, Y.80, Q.82, W.121, E.141, V.142, T.143, Q.144, E.162, T.164, G.166, E.168, R.169 Chain F: A.76 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:T.39, B:R.64, B:D.67, B:D.67, B:L.77, B:Y.80, B:Q.82, B:T.143, B:E.162, B:G.166, B:R.169 Salt bridges: B:R.64 pi-Stacking: B:Y.80, B:Y.80 pi-Cation interactions: B:R.169

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

MG.2: 3 residues within 4Å: Chain A: D.119, E.134, E.141 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.119, A:E.134 MG.4: 3 residues within 4Å: Chain B: D.119, E.134 Chain F: A.76 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.119, B:E.134 MG.5: 1 residues within 4Å: Chain A: E.134 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain C: D.425, N.446 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.425 MG.7: 2 residues within 4Å: Chain D: D.474 Chain F: G.1 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.474 MG.8: 3 residues within 4Å: Chain E: U.8, A.9, U.12 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Han, L. et al., The binding mode of orphan glycyl-tRNA synthetase with tRNA supports the synthetase classification and reveals large domain movements. Sci Adv (2023)

Release Date

2023-02-01

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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