SMTL ID : 5on3.1 (1 other biounit)

Quaternary complex of mutant T252A of E. coli leucyl-tRNA synthetase with tRNA(leu), leucyl-adenylate analogue, and post-transfer editing analogue of leucine in the aminoacylation conformation

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.179, D.182, C.196, C.199, T.201 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.179, A:D.182, A:C.196, A:C.199

1 x LSS: 5'-O-(L-leucylsulfamoyl)adenosine(Non-covalent)

LSS.2: 24 residues within 4Å: Chain A: M.60, L.61, P.62, Y.63, H.69, G.71, H.72, N.75, Y.76, D.100, S.516, Y.519, G.549, G.550, E.552, H.553, H.557, Q.586, G.587, M.588, V.589, K.639, M.640 Chain B: A.87 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:L.61, A:Y.63, A:D.100, A:G.550, A:E.552, A:E.552, A:Q.586, A:V.589, A:V.589, A:M.640 Salt bridges: A:H.72

1 x 9YN: (2~{S})-~{N}-[(2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-(hydroxymethyl)-4-oxidanyl-oxolan-3-yl]-2-azanyl-4-methyl-pentanamide(Non-covalent)

9YN.3: 14 residues within 4Å: Chain A: Y.266, T.267, T.268, R.269, F.345, V.346, L.347, Y.350, V.355, M.356, A.357, V.358, H.361, D.365 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:R.269, A:R.269, A:V.358 Hydrogen bonds: A:T.268, A:L.347, A:L.347, A:Y.350, A:Y.350, A:V.358, A:D.365 pi-Stacking: A:Y.350

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dulic, M. et al., Kinetic Origin of Substrate Specificity in Post-Transfer Editing by Leucyl-tRNA Synthetase. J. Mol. Biol. (2018)

Release Date

2017-11-15

Peptides

Leucine--tRNA ligase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Leucine--tRNA ligase

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