SMTL ID : 4o2d.1

Crystal structure of aspartyl-tRNA synthetase from Mycobacterium smegmatis with bound aspartic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

2 x ASP: ASPARTIC ACID(Non-covalent)

ASP.1: 14 residues within 4Å: Chain A: E.192, S.214, Q.216, K.219, R.238, Q.252, H.470, H.471, G.507, G.508, R.511, G.552, I.553, A.554 13 PLIP interactions: 12 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:A.554 Hydrogen bonds: A:E.192, A:S.214, A:Q.252, A:I.553, D.1 Water bridges: A:K.219, A:R.238 Salt bridges: A:K.219, A:R.238, A:H.470, A:H.471, A:R.511 ASP.4: 14 residues within 4Å: Chain B: E.192, S.214, Q.216, K.219, R.238, Q.252, H.470, H.471, G.507, G.508, R.511, G.552, I.553, A.554 11 PLIP interactions: 10 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:A.554 Hydrogen bonds: B:E.192, B:S.214, B:Q.252, B:I.553, D.4 Salt bridges: B:K.219, B:R.238, B:H.470, B:H.471, B:R.511

4 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.2: 5 residues within 4Å: Chain A: D.303, M.469, H.470, D.497, E.504 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.303, A:H.470, A:D.497 TRS.3: 3 residues within 4Å: Chain A: D.52, H.53, G.54 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.54 TRS.5: 3 residues within 4Å: Chain B: R.49, R.51, H.53 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.49, B:R.49, B:R.51, B:R.51, B:H.53 TRS.6: 3 residues within 4Å: Chain B: R.85, A.86, Q.132 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.85, B:A.86

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Baugh, L. et al., Increasing the structural coverage of tuberculosis drug targets. Tuberculosis (Edinb) (2015)

Release Date

2014-01-22

Peptides

Aspartate--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Aspartate--tRNA ligase