SMTL ID : 1b8a.1

ASPARTYL-TRNA SYNTHETASE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

6 x MN: MANGANESE (II) ION(Non-covalent)(Non-functional Binders)

MN.1: 2 residues within 4Å: Chain A: H.223 Ligands: ATP.4 No protein-ligand interaction detected (PLIP) MN.2: 5 residues within 4Å: Chain A: D.354, E.361, S.364 Ligands: MN.3, ATP.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.361, A:S.364, H2O.6, H2O.6 MN.3: 3 residues within 4Å: Chain A: E.361 Ligands: MN.2, ATP.4 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.361, H2O.5, H2O.5, H2O.6 MN.5: 1 residues within 4Å: Ligands: ATP.8 No protein-ligand interaction detected (PLIP) MN.6: 3 residues within 4Å: Chain B: E.361 Ligands: MN.7, ATP.8 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.361, H2O.29, H2O.29, H2O.30 MN.7: 5 residues within 4Å: Chain B: D.354, E.361, S.364 Ligands: MN.6, ATP.8 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.361, B:S.364, H2O.29, H2O.29

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

ATP.4: 16 residues within 4Å: Chain A: R.214, E.216, R.222, H.223, L.224, A.227, E.361, I.362, S.363, S.364, G.407, G.409, R.412 Ligands: MN.1, MN.2, MN.3 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:E.216, A:L.224, A:E.361, A:I.362, A:G.409, A:R.412 Water bridges: A:R.214, A:R.214, A:R.214, A:R.214, A:R.214, A:R.214, A:K.336 Salt bridges: A:R.214, A:R.214, A:R.222, A:H.223, A:R.412 pi-Cation interactions: A:R.412, A:R.412 ATP.8: 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: MN.5, MN.6, MN.7 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:E.216, B:L.224, B:E.361, B:I.362, B:S.364, B:G.409, B:R.412 Water bridges: B:R.214, 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, B:R.412

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

1999-02-02

Peptides

PROTEIN (ASPARTYL-TRNA SYNTHETASE): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PROTEIN (ASPARTYL-TRNA SYNTHETASE)