SMTL ID : 3nem.1

Aspartyl-tRNA synthetase complexed with aspartyl adenylate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-dimer

Ligands

1 x AMO: ASPARTYL-ADENOSINE-5'-MONOPHOSPHATE(Non-covalent)

AMO.1: 22 residues within 4Å: Chain A: E.170, S.190, Q.192, K.195, R.214, E.216, H.223, L.224, A.227, Y.339, E.361, I.362, S.363, S.364, G.365, R.368, G.405, F.406, G.407, G.409, R.412, I.423 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:S.190, A:Q.192, A:E.216, A:L.224, A:Y.339, A:Y.339, A:S.364, A:G.409, A:R.412 Water bridges: A:E.170, A:R.214, A:S.229, A:K.336, A:E.361 Salt bridges: A:K.195, A:R.214, A:R.214, A:R.368 pi-Cation interactions: A:R.412

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

ATP.2: 16 residues within 4Å: Chain B: R.214, E.216, H.223, L.224, A.227, E.361, I.362, S.363, S.364, G.407, G.409, R.412, I.423 Ligands: MG.3, MG.4, MG.5 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:E.216, B:L.224, B:E.361, B:E.361, B:S.364, B:S.364, B:G.409 Water bridges: B:R.214, B:R.214, B:R.214, B:R.214, B:R.214 Salt bridges: B:R.214, B:R.214, B:H.223, B:R.412 pi-Cation interactions: B:R.412

3 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.3: 1 residues within 4Å: Ligands: ATP.2 No protein-ligand interaction detected (PLIP) MG.4: 3 residues within 4Å: Chain B: E.361 Ligands: ATP.2, MG.5 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.361, H2O.15, H2O.15, H2O.16 MG.5: 5 residues within 4Å: Chain B: D.354, E.361, S.364 Ligands: ATP.2, MG.4 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.361, H2O.15, H2O.16

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schmitt, E. et al., Crystal structure of aspartyl-tRNA synthetase from Pyrococcus kodakaraensis KOD: archaeon specificity and catalytic mechanism of adenylate formation. Embo J. (1998)

Release Date

2010-08-04

Peptides

Aspartyl-tRNA synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Aspartyl-tRNA synthetase

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