SMTL ID : 2xti.1

Asparaginyl-tRNA synthetase from Brugia malayi complexed with ATP:Mg and L-Asp-beta-NOH adenylate:PPi:Mg

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

1 x NB8: 5'-O-[(R)-{[(2S)-2-amino-4-(hydroxyamino)-4-oxobutanoyl]oxy}(hydroxy)phosphoryl]adenosine(Non-covalent)

NB8.1: 26 residues within 4Å: Chain A: E.167, S.187, Q.189, R.210, E.212, R.218, H.219, L.220, Y.223, H.225, E.227, E.229, Y.337, E.360, I.361, V.362, G.363, G.364, R.367, G.404, Y.405, G.406, G.408, R.411 Ligands: POP.2, MG.3 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:E.167, A:S.187, A:Q.189, A:E.212, A:L.220, A:Y.223, A:E.227, A:E.229, A:E.360, A:V.362, A:R.367, A:R.367, A:G.408, A:R.411 Water bridges: A:Y.337 Salt bridges: A:R.210, A:R.210, A:H.225 pi-Stacking: A:Y.223 pi-Cation interactions: A:R.411, A:R.411

1 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.2: 8 residues within 4Å: Chain A: R.218, H.219, E.360, R.411 Ligands: NB8.1, MG.3, MG.4, MG.5 9 PLIP interactions: 9 interactions with chain A Water bridges: A:R.210, A:R.210, A:R.218, A:E.310, A:D.352, A:E.360 Salt bridges: A:R.218, A:H.219, A:R.411

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

MG.3: 3 residues within 4Å: Chain A: E.360 Ligands: NB8.1, POP.2 4 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: A:E.360, NB8.1, H2O.6, H2O.6 MG.4: 1 residues within 4Å: Ligands: POP.2 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain A: I.308 Ligands: POP.2 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain B: E.360 Ligands: ATP.6, MG.9 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.360 MG.8: 3 residues within 4Å: Chain B: E.212, H.219 Ligands: ATP.6 No protein-ligand interaction detected (PLIP) MG.9: 4 residues within 4Å: Chain B: D.352, E.360 Ligands: ATP.6, MG.7 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.360

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

ATP.6: 18 residues within 4Å: Chain B: R.210, E.212, R.218, H.219, L.220, Y.223, H.225, E.360, I.361, V.362, G.363, G.406, G.408, R.411, I.422 Ligands: MG.7, MG.8, MG.9 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:R.210, B:E.212, B:E.212, B:L.220, B:E.360, B:V.362, B:G.408, B:R.411 Salt bridges: B:R.210, B:R.218, B:H.219, B:R.411 pi-Stacking: B:Y.223, B:Y.223 pi-Cation interactions: B:R.411, B:R.411

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Crepin, T. et al., A Hybrid Structural Model of the Complete Brugia Malayi Cytoplasmic Asparaginyl-tRNA Synthetase. J.Mol.Biol. (2011)

Release Date

2010-12-15

Peptides

ASPARAGINYL-TRNA SYNTHETASE\, CYTOPLASMIC\, PUTATIVE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ASPARAGINYL-TRNA SYNTHETASE\, CYTOPLASMIC\, PUTATIVE