SMTL ID : 1x55.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 6 residues within 4Å: Chain A: R.211, H.220, E.357, R.408 Ligands: MG.2, NSS.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.211, A:E.357, A:E.357 Water bridges: A:R.219, A:R.408 Salt bridges: A:H.220, A:R.408 PO4.5: 6 residues within 4Å: Chain B: R.211, H.220, E.357, R.408 Ligands: MG.6, NSS.8 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.211, B:E.357, B:E.357 Water bridges: B:R.219, B:R.408 Salt bridges: B:H.220, B:R.408

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: E.357 Ligands: PO4.1, NSS.4 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.357, H2O.25, H2O.30, H2O.49 MG.3: 2 residues within 4Å: Chain A: D.303, D.348 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain B: E.357 Ligands: PO4.5, NSS.8 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.357, H2O.393, H2O.398, H2O.417 MG.7: 2 residues within 4Å: Chain B: D.303, D.348 No protein-ligand interaction detected (PLIP)

2 x NSS: 5'-O-[N-(L-ASPARAGINYL)SULFAMOYL]ADENOSINE(Non-covalent)

NSS.4: 25 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, G.401, F.402, G.403, G.405, R.408, I.419 Ligands: PO4.1, MG.2 28 PLIP interactions: 28 interactions with chain A Hydrogen bonds: A:E.168, A:E.168, A:E.168, A:S.188, A:R.211, A:L.221, A:L.221, A:E.228, A:E.228, A:Y.333, A:I.358, A:I.359, A:R.364, A:R.364, A:G.405, A:R.408 Water bridges: A:E.168, A:E.168, A:E.168, A:R.211, A:Y.333, A:G.360, A:F.402, A:F.402 Salt bridges: A:R.211 pi-Stacking: A:F.224, A:F.224 pi-Cation interactions: A:R.408 NSS.8: 25 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, G.401, F.402, G.403, G.405, R.408, I.419 Ligands: PO4.5, MG.6 25 PLIP interactions: 25 interactions with chain B Hydrogen bonds: B:E.168, B:E.168, B:S.188, B:R.211, B:L.221, B:L.221, B:E.228, B:I.358, B:I.359, B:R.364, B:R.364, B:G.405, B:R.408 Water bridges: B:E.168, B:E.168, B:E.168, B:R.211, B:Y.333, B:G.360, B:F.402, B:F.402 Salt bridges: B:R.211 pi-Stacking: B:F.224, B:F.224 pi-Cation interactions: B:R.408

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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