SMTL ID : 5e6m.1

Crystal structure of human wild type GlyRS bound with tRNAGly

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.93 Å

Oligo State

homo-dimer

Ligands

2 x GAP: GLYCYL-ADENOSINE-5'-PHOSPHATE(Non-covalent)

GAP.1: 20 residues within 4Å: Chain A: E.245, R.277, E.279, L.286, I.287, R.288, V.289, F.292, M.294, E.296, E.403, I.404, V.405, G.406, R.410, E.522, S.524, G.526, R.529 Chain D: A.74 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:E.245, A:R.277, A:E.279, A:V.289, A:V.289, A:E.403, A:G.406, A:R.410, A:S.524, A:S.524, A:G.526, A:R.529 Salt bridges: A:R.277 pi-Stacking: A:F.292, A:F.292 pi-Cation interactions: A:R.529, A:R.529 GAP.3: 20 residues within 4Å: Chain B: E.245, R.277, E.279, L.286, I.287, R.288, V.289, F.292, M.294, E.296, E.403, I.404, V.405, G.406, R.410, E.522, S.524, G.526, R.529 Chain C: A.74 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:E.245, B:E.279, B:V.289, B:E.403, B:E.403, B:G.526, B:R.529 Water bridges: B:R.529 Salt bridges: B:R.277, B:R.277 pi-Stacking: B:F.292, B:F.292 pi-Cation interactions: B:R.529, B:R.529

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

SO4.2: 8 residues within 4Å: Chain A: Y.94, K.104, N.274, E.291, T.293 Chain B: D.125, C.126, T.127 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.274, A:E.291, A:T.293, B:D.125 Water bridges: A:T.293 Salt bridges: A:K.104

2 x NI: NICKEL (II) ION(Non-functional Binders)

NI.4: 3 residues within 4Å: Chain C: U.8, G.9, G.12 No protein-ligand interaction detected (PLIP) NI.5: 3 residues within 4Å: Chain D: U.8, G.9, G.12 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Qin, X. et al., Crystal Structure of the Wild-Type Human GlyRS Bound with tRNA(Gly) in a Productive Conformation. J.Mol.Biol. (2016)

Release Date

2016-07-20

Peptides

Glycine--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glycine--tRNA ligase

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