SMTL ID : 1x54.1

Crystal structure of asparaginyl-tRNA synthetase from Pyrococcus horikoshii complexed with asparaginyl-adenylate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: E.357 Ligands: 4AD.2 6 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions, 4 Ligand-Water interactions Metal complexes: A:E.357, 4AD.2, H2O.73, H2O.301, H2O.302, H2O.304 MG.4: 2 residues within 4Å: Chain B: E.357 Ligands: 4AD.5 6 PLIP interactions: 1 interactions with chain B, 1 Ligand-Ligand interactions, 4 Ligand-Water interactions Metal complexes: B:E.357, 4AD.5, H2O.382, H2O.610, H2O.611, H2O.613

2 x 4AD: 4-AMINO-1,4-DIOXOBUTAN-2-AMINIUM ADENOSINE-5'-MONOPHOSPHATE(Non-covalent)

4AD.2: 23 residues within 4Å: Chain A: V.167, E.168, S.188, Q.190, R.211, R.219, H.220, L.221, F.224, H.226, E.228, Y.333, E.357, I.358, I.359, G.360, R.364, F.402, G.403, G.405, R.408, I.419 Ligands: MG.1 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:E.168, A:E.168, A:S.188, A:L.221, A:L.221, A:E.228, A:E.228, A:Y.333, A:E.357, A:I.359, A:R.364, A:R.364, A:G.405, A:R.408 Water bridges: A:R.211, A:F.402, A:F.402 Salt bridges: A:R.211, A:R.211, A:H.226 pi-Stacking: A:F.224, A:F.224 pi-Cation interactions: A:R.408, A:R.408 4AD.5: 23 residues within 4Å: Chain B: V.167, E.168, S.188, Q.190, R.211, R.219, H.220, L.221, F.224, H.226, E.228, Y.333, E.357, I.358, I.359, G.360, R.364, F.402, G.403, G.405, R.408, I.419 Ligands: MG.4 22 PLIP interactions: 22 interactions with chain B Hydrogen bonds: B:E.168, B:S.188, B:L.221, B:L.221, B:E.228, B:E.357, B:E.357, B:I.359, B:R.364, B:R.364, B:G.405, B:R.408 Water bridges: B:E.168, B:F.402, B:F.402 Salt bridges: B:R.211, B:R.211, B:H.226 pi-Stacking: B:F.224, B:F.224 pi-Cation interactions: B:R.408, B:R.408

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.3: 5 residues within 4Å: Chain A: D.366, D.367, S.396 Chain B: I.98, Q.99 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:D.366, B:Q.99 Hydrogen bonds: A:D.366, A:D.366, A:S.396 Water bridges: B:Q.99 MPD.6: 5 residues within 4Å: Chain A: I.98, Q.99 Chain B: D.366, D.367, S.396 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:D.366, A:Q.99 Hydrogen bonds: B:D.366, B:D.366, B:S.396 Water bridges: A:Q.99

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Iwasaki, W. et al., Structural Basis of the Water-assisted Asparagine Recognition by Asparaginyl-tRNA Synthetase. J.Mol.Biol. (2006)

Release Date

2006-05-23

Peptides

Asparaginyl-tRNA synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Asparaginyl-tRNA synthetase

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