SMTL ID : 1obc.1

LEUCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH A POST-TRANSFER EDITING SUBSTRATE ANALOGUE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x LEU: LEUCINE(Non-covalent)

LEU.1: 11 residues within 4Å: Chain A: M.40, F.41, P.42, Y.43, D.80, S.504, Y.507, Y.535, H.541, H.545 Ligands: LMS.6 4 PLIP interactions: 4 interactions with chain A, Hydrophobic interactions: A:F.41, A:H.545 Hydrogen bonds: A:D.80, A:D.80

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 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.3: 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 NVA: NORVALINE(Non-covalent)

NVA.4: 9 residues within 4Å: Chain A: T.247, R.249, T.252, M.338, V.340, H.343, D.344, D.347 Ligands: 2AD.5 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:R.249, A:V.340, A:V.340 Hydrogen bonds: A:M.338 Water bridges: A:D.347

1 x 2AD: 2'-AMINO-2'-DEOXYADENOSINE(Non-covalent)

2AD.5: 11 residues within 4Å: Chain A: F.246, T.247, T.248, Y.327, V.328, L.329, Y.332, G.335, I.337, R.346 Ligands: NVA.4 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:T.248, A:T.248, A:L.329, A:L.329, A:Y.332, A:G.335, A:R.346 Water bridges: A:T.248, A:A.336, A:D.344, A:R.346 pi-Stacking: A:Y.332

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

LMS.6: 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 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:F.41, A:Y.43, A:G.538, A:E.540, A:Q.574, A:V.577, A:V.577, A:M.638

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lincecum, T. et al., Structural and Mechanistic Basis of Pre- and Posttransfer Editing by Leucyl-tRNA Synthetase. Mol.Cell (2003)

Release Date

2003-05-09

Peptides

LEUCYL-TRNA SYNTHETASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

LEUCYL-TRNA SYNTHETASE

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