SMTL ID : 2zt7.1

Crystal structure of human Glycyl-tRNA synthetase (GlyRS) in complex with Glycine and ATP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

2 x GLY: GLYCINE(Non-covalent)

GLY.1: 8 residues within 4Å: Chain A: E.245, R.277, E.296, Y.386, R.410, E.522, S.524 Ligands: ATP.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.245, A:E.296, A:E.296, A:Y.386, A:R.410, A:S.524 Salt bridges: A:R.277 GLY.3: 8 residues within 4Å: Chain B: E.245, R.277, E.296, Y.386, R.410, E.522, S.524 Ligands: ATP.4 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.245, B:E.245, B:E.296, B:R.410, B:S.524 Salt bridges: B:R.277

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.2: 16 residues within 4Å: Chain A: R.159, R.277, E.279, I.287, R.288, V.289, F.292, Y.386, E.403, I.404, V.405, G.406, S.524, G.526, R.529 Ligands: GLY.1 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:E.279, A:V.289, A:Y.386, A:E.403, A:E.403, A:E.403, A:R.529 Water bridges: A:R.277 Salt bridges: A:R.159, A:R.277, A:R.277, A:R.288, A:R.529 pi-Stacking: A:F.292, A:F.292 pi-Cation interactions: A:R.529, A:R.529 ATP.4: 16 residues within 4Å: Chain B: R.159, R.277, E.279, I.287, R.288, V.289, F.292, Y.386, E.403, I.404, V.405, G.406, S.524, G.526, R.529 Ligands: GLY.3 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:E.279, B:V.289, B:E.403, B:E.403, B:E.403, B:R.529 Water bridges: B:R.277 Salt bridges: B:R.159, B:R.277, B:R.277, B:R.288, B:R.529 pi-Stacking: B:F.292, B:F.292 pi-Cation interactions: B:R.529, B:R.529

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guo, R.T. et al., Crystal structures and biochemical analyses suggest unique mechanism and role for human GlyRS in Ap4A homeostasis. To be Published

Release Date

2009-08-25

Peptides

Glycyl-tRNA synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Glycyl-tRNA synthetase

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