SMTL ID : 3zgz.1 (1 other biounit)

Ternary complex of E. coli leucyl-tRNA synthetase, tRNA(leu) and toxic moiety from agrocin 84 (TM84) in aminoacylation-like conformation

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.179, D.182, C.196, C.199 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.179, A:C.199

1 x 84T: [(2S,4S,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-oxolan-2-yl]methoxy-N-[(2S,3R)-4-methyl-2,3-bis(oxidanyl)pentanoyl]phosphonamidic acid(Non-covalent)

84T.2: 26 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, F.513, S.516, Y.519, Y.547, G.550, E.552, H.553, H.557, Q.586, G.587, M.588, V.589, K.639, M.640, K.642 Chain B: A.88 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.61, A:F.513 Hydrogen bonds: A:L.61, A:Y.63, A:Y.63, A:G.550, A:E.552, A:V.589, A:V.589, A:M.640, A:K.642

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

MG.3: 2 residues within 4Å: Chain B: U.21, U.72 No protein-ligand interaction detected (PLIP) MG.4: 1 residues within 4Å: Chain B: G.47 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain B: U.9, G.10 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain B: U.9, G.14 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain B: U.60, C.62 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chopra, S. et al., Plant Tumour Biocontrol Agent Employs a tRNA-Dependent Mechanism to Inhibit Leucyl-tRNA Synthetase. Nat.Commun. (2013)

Release Date

2013-01-30

Peptides

LEUCINE--TRNA LIGASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

LEUCINE--TRNA LIGASE

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