SMTL ID : 6sjc.1

Structure of T. thermophilus AspRS in Complex with 5'-O-(N-(L-aspartyl)-sulfamoyl)adenosine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.23 Å

Oligo State

homo-dimer

Ligands

2 x DSZ: 5'-O-(L-alpha-aspartylsulfamoyl)adenosine(Non-covalent)

DSZ.1: 23 residues within 4Å: Chain A: S.200, Q.202, K.205, R.224, E.226, D.231, R.232, Q.233, F.236, Q.238, H.443, H.444, E.477, V.478, G.479, G.480, G.481, R.484, G.525, I.526, A.527, G.529, R.532 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:A.527 Hydrogen bonds: A:S.200, A:Q.202, A:R.224, A:E.226, A:Q.233, A:Q.238, A:E.477, A:G.529, A:R.532, A:R.532 Water bridges: A:K.205, A:H.443, A:H.444, A:G.480, A:D.531 Salt bridges: A:K.205, A:R.224, A:H.443, A:H.444, A:R.484 pi-Stacking: A:F.236, A:F.236 pi-Cation interactions: A:R.532 DSZ.2: 24 residues within 4Å: Chain B: E.178, S.200, Q.202, K.205, R.224, E.226, D.231, R.232, Q.233, F.236, Q.238, H.444, E.477, V.478, G.479, G.480, G.481, R.484, G.525, I.526, A.527, W.528, G.529, R.532 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:A.527 Hydrogen bonds: B:E.178, B:E.178, B:S.200, B:R.224, B:Q.233, B:Q.233, B:Q.238, B:E.477, B:I.526, B:G.529, B:R.532, B:R.532 Water bridges: B:D.531 Salt bridges: B:K.205, B:R.224, B:H.444, B:R.484 pi-Stacking: B:F.236, B:F.236 pi-Cation interactions: B:R.532

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pang, L. et al., Structural Insights into the Binding of Natural Pyrimidine-Based Inhibitors of Class II Aminoacyl-tRNA Synthetases. Acs Chem.Biol. (2020)

Release Date

2020-01-08

Peptides

Aspartate--tRNA(Asp) ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Aspartate--tRNA(Asp) ligase

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