SMTL ID : 2v0c.1

LEUCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH A SULPHAMOYL ANALOGUE OF LEUCYL-ADENYLATE In the synthetic site and an adduct of AMP with 5-Fluoro-1,3-dihydro-1-hydroxy-2,1-benzoxaborole (AN2690) in the editing site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

1 x LEU: LEUCINE(Non-covalent)

LEU.1: 12 residues within 4Å: Chain A: M.40, F.41, P.42, Y.43, D.80, F.501, S.504, Y.507, Y.535, H.541, H.545 Ligands: LMS.2 8 PLIP interactions: 8 interactions with chain A, Hydrophobic interactions: A:M.40, A:F.41, A:F.41, A:F.501, A:H.545 Hydrogen bonds: A:Y.43, A:D.80 Water bridges: A:E.540

1 x LMS: [(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDRO-2-FURANYL]METHYL SULFAMATE(Non-covalent)

LMS.2: 19 residues within 4Å: Chain A: M.40, F.41, P.42, Y.43, H.49, G.51, H.52, N.55, Y.56, G.537, G.538, E.540, Q.574, G.575, M.576, V.577, V.637, M.638 Ligands: LEU.1 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Y.43, A:G.538, A:E.540, A:Q.574, A:V.577, A:V.577, A:M.638 Water bridges: A:E.540, A:E.540

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: C.439, C.442, C.484, C.487 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.439, A:C.442, A:C.484, A:C.487 ZN.4: 4 residues within 4Å: Chain A: C.159, C.162, C.176, H.179 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.159, A:C.162, A:C.176, A:H.179

1 x ANZ: [(6-AMINO-9H-PURIN-9-YL)-[5-FLUORO-1,3-DIHYDRO-1-HYDROXY-2,1-BENZOXABOROLE]-4'YL]METHYL DIHYDROGEN PHOSPHATE(Non-covalent)

ANZ.5: 15 residues within 4Å: Chain A: F.246, T.247, T.248, R.249, T.252, Y.327, V.328, L.329, Y.332, I.337, M.338, V.340, H.343, D.344, R.346 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:R.249, A:R.249, A:V.340, A:D.344 Hydrogen bonds: A:T.247, A:T.248, A:L.329, A:L.329, A:D.344, A:R.346, A:R.346 Water bridges: A:G.335

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

SO4.6: 4 residues within 4Å: Chain A: L.714, E.715, G.716, R.719 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.716 Water bridges: A:E.715, A:R.719, A:R.719 Salt bridges: A:R.719 SO4.7: 4 residues within 4Å: Chain A: G.707, R.769, R.773, W.795 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.707, A:W.795 Salt bridges: A:R.769, A:R.773 SO4.8: 5 residues within 4Å: Chain A: L.207, E.208, E.214, K.217, R.221 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.208, A:E.214 Salt bridges: A:K.217, A:R.221 SO4.9: 4 residues within 4Å: Chain A: R.300, E.301, K.302, K.353 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.302 Salt bridges: A:K.353 SO4.10: 1 residues within 4Å: Chain A: R.759 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.759, A:R.759 Salt bridges: A:R.759

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rock, F. et al., An Antifungal Agent Inhibits an Aminoacyl-tRNA Synthetase by Trapping tRNA in the Editing Site. Science (2007)

Release Date

2007-07-03

Peptides

AMINOACYL-TRNA SYNTHETASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

AMINOACYL-TRNA SYNTHETASE