SMTL ID : 3wqy.1

Crystal structure of Archaeoglobus fulgidus alanyl-tRNA synthetase in complex with wild-type tRNA(Ala) having G3.U70

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

homo-dimer

Ligands

2 x A5A: '5'-O-(N-(L-ALANYL)-SULFAMOYL)ADENOSINE(Non-covalent)

A5A.1: 18 residues within 4Å: Chain A: A.99, R.128, D.131, H.141, L.142, F.145, M.147, W.191, E.209, V.210, A.211, T.212, V.214, D.242, G.244, G.246, R.249 Chain C: A.75 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:R.128, A:R.128, A:D.131, A:L.142, A:L.142, A:E.209, A:V.210, A:T.212, A:T.212, A:T.212, A:D.242, A:G.246, A:R.249 Salt bridges: A:R.128 pi-Stacking: A:F.145, A:F.145 pi-Cation interactions: A:R.249 A5A.2: 19 residues within 4Å: Chain B: A.99, R.128, D.131, R.140, H.141, L.142, F.145, M.147, W.191, E.209, V.210, A.211, T.212, V.214, D.242, T.243, G.244, G.246, R.249 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:R.128, B:D.131, B:D.131, B:L.142, B:V.210, B:T.212, B:T.212, B:T.212, B:D.242, B:G.246 Salt bridges: B:R.128 pi-Stacking: B:F.145, B:F.145 pi-Cation interactions: B:R.249

3 x MG: MAGNESIUM ION(Non-functional Binders)

MG.3: 3 residues within 4Å: Chain C: C.47, A.58, U.59 No protein-ligand interaction detected (PLIP) MG.4: 4 residues within 4Å: Chain C: U.8, A.9, C.11, U.12 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain C: G.38, G.39 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Naganuma, M. et al., The selective tRNA aminoacylation mechanism based on a single G.U pair. Nature (2014)

Release Date

2014-06-18

Peptides

Alanine--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Alanine--tRNA ligase

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