SMTL ID : 1nyr.1

Structure of Staphylococcus aureus threonyl-tRNA synthetase complexed with ATP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.336, H.387, Y.468, H.517 Ligands: THR.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:C.336, A:H.387, A:H.517, THR.4 ZN.2: 4 residues within 4Å: Chain A: H.75, H.79, C.181, H.185 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.75, A:H.79, A:C.181, A:H.185 ZN.5: 4 residues within 4Å: Chain B: C.336, H.387, H.517 Ligands: THR.7 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:C.336, B:H.387, B:H.517, THR.7

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.3: 17 residues within 4Å: Chain A: R.365, E.367, Q.376, R.377, V.378, M.381, L.383, K.471, E.484, T.485, L.486, T.488, Q.490, S.522, T.523, R.526 Ligands: THR.4 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:Y.313, A:Y.313, A:R.365, A:E.367, A:V.378, A:T.485, A:T.485, A:T.523, A:R.526 Water bridges: A:R.377, A:R.377, A:T.485 Salt bridges: A:R.365, A:R.365, A:R.377, A:K.471, A:K.471, A:R.526 pi-Cation interactions: A:R.526 ATP.6: 15 residues within 4Å: Chain B: Y.313, M.363, R.365, E.367, Q.376, R.377, V.378, M.381, L.383, E.464, T.485, S.522, T.523, R.526 Ligands: THR.7 17 PLIP interactions: 16 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: B:R.365, B:E.367, B:R.377, B:V.378, B:V.378, B:T.485, B:T.523, B:R.526, T.7 Water bridges: B:K.471, B:R.526 Salt bridges: B:R.365, B:R.365, B:R.365, B:K.471 pi-Cation interactions: B:R.526, B:R.526

2 x THR: THREONINE(Non-covalent)

THR.4: 14 residues within 4Å: Chain A: M.334, N.335, C.336, M.363, R.365, L.383, D.385, H.387, Y.468, Q.490, H.517, R.518 Ligands: ZN.1, ATP.3 9 PLIP interactions: 6 interactions with chain A, 3 Ligand-Ligand interactions Hydrophobic interactions: A:L.383, A:H.517 Hydrogen bonds: A:N.335, A:C.336, A:Q.490, T.4, T.4, T.4 Salt bridges: A:R.365 THR.7: 12 residues within 4Å: Chain B: M.334, C.336, M.363, R.365, L.383, D.385, H.387, Y.468, Q.490, H.517 Ligands: ZN.5, ATP.6 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions Water bridges: B:D.385, T.7 Salt bridges: B:R.365

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Torres-Larios, A. et al., Conformational movements and cooperativity upon amino acid, ATP and tRNA binding in threonyl-tRNA synthetase. J.Mol.Biol. (2003)

Release Date

2003-10-28

Peptides

threonyl-tRNA synthetase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

threonyl-tRNA synthetase 1

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