SMTL ID : 1obh.1

LEUCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH A PRE-TRANSFER EDITING SUBSTRATE ANALOGUE IN BOTH SYNTHETIC ACTIVE SITE AND EDITING SITE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: L.714, E.715, G.716, R.719 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.716 Salt bridges: A:R.719 SO4.2: 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 SO4.3: 3 residues within 4Å: Chain A: V.564, E.565, E.566 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.565, A:E.566 SO4.4: 1 residues within 4Å: Chain A: R.759 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.759 SO4.5: 4 residues within 4Å: Chain A: L.84, R.426, R.428, D.499 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.426, A:R.428 SO4.6: 5 residues within 4Å: Chain A: H.49, H.52, M.638, S.639, K.640 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.640 Water bridges: A:S.641 Salt bridges: A:H.49, A:H.52

1 x HG: MERCURY (II) ION(Non-covalent)

HG.7: 3 residues within 4Å: Chain A: Y.102, C.128, E.129 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.128

2 x NVA: NORVALINE(Non-covalent)

NVA.8: 8 residues within 4Å: Chain A: M.40, F.41, P.42, Y.43, D.80, Y.535, H.545 Ligands: LMS.9 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.41 Hydrogen bonds: A:D.80 NVA.10: 10 residues within 4Å: Chain A: T.247, R.249, T.252, I.337, M.338, V.340, H.343, D.344, D.347 Ligands: LMS.11 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:R.249, A:V.340, A:V.340, A:D.344 Hydrogen bonds: A:T.247, A:D.347

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

LMS.9: 17 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, G.575, M.576, V.577, V.637, M.638 Ligands: NVA.8 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:F.41, A:Y.43, A:G.538, A:V.577, A:V.577, A:M.638 LMS.11: 10 residues within 4Å: Chain A: T.247, T.248, R.249, Y.327, V.328, L.329, Y.332, I.337, D.344 Ligands: NVA.10 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.247, A:T.248, A:R.249, A:L.329, A:L.329, A:D.344 Water bridges: A:D.344, A:D.344

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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