SMTL ID : 3wqz.1

Crystal structure of Archaeoglobus fulgidus alanyl-tRNA synthetase in complex with a tRNA(Ala) variant having A3.U70

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.49 Å

Oligo State

homo-dimer

Ligands

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

A5A.1: 16 residues within 4Å: Chain A: A.99, R.128, H.141, L.142, F.145, M.147, W.191, E.209, V.210, A.211, T.212, D.242, T.243, G.244, G.246, R.249 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:R.128, A:L.142, A:L.142, A:E.209, 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.3: 19 residues within 4Å: Chain B: A.99, I.101, 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, T.243, G.244, G.246, R.249 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:R.128, B:R.128, B:D.131, B:D.131, B:L.142, B:E.209, B:T.212, B:T.212, B:D.242, B:G.246, B:R.249 Salt bridges: B:R.128 pi-Stacking: B:F.145, B:F.145

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 2 residues within 4Å: Chain A: H.604, C.703 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.604, A:C.703 ZN.4: 4 residues within 4Å: Chain B: H.600, H.604, Q.701, C.703 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.600, B:H.604, B:C.703

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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