SMTL ID : 5dk4.1

Crystal structure analysis of Tryptophanyl-trna synthetase from Bacillus stearothermophilus in complex with indolmycin and Mg*ATP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

ATP.1: 24 residues within 4Å: Chain A: G.8, I.9, Q.10, S.12, G.18, N.19, G.22, A.23, K.112, V.144, G.145, D.147, Q.148, G.181, A.182, R.183, I.184, K.193, M.194, S.195, K.196, S.197 Ligands: MG.2, 5BX.4 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:Q.10, A:Q.10, A:S.12, A:N.19, A:G.145, A:I.184, A:I.184, A:K.193, A:K.196, A:S.197, A:S.197, A:S.197 Water bridges: A:N.19, A:K.112, A:K.112, A:K.112, A:K.112, A:K.112, A:E.146, A:S.195 Salt bridges: A:K.112, A:K.193, A:K.193, A:K.196, A:K.196, A:K.196 ATP.5: 24 residues within 4Å: Chain B: G.8, I.9, Q.10, S.12, G.18, N.19, G.22, A.23, K.112, V.144, G.145, D.147, Q.148, G.181, A.182, R.183, I.184, K.193, M.194, S.195, K.196, S.197 Ligands: MG.6, 5BX.8 26 PLIP interactions: 26 interactions with chain B Hydrogen bonds: B:Q.10, B:Q.10, B:S.12, B:N.19, B:G.145, B:I.184, B:I.184, B:K.193, B:K.196, B:S.197, B:S.197, B:S.197 Water bridges: B:N.19, B:K.112, B:K.112, B:K.112, B:K.112, B:K.112, B:E.146, B:S.195 Salt bridges: B:K.112, B:K.193, B:K.193, B:K.196, B:K.196, B:K.196

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: Q.10, K.112, K.193 Ligands: ATP.1, 5BX.4 No protein-ligand interaction detected (PLIP) MG.6: 5 residues within 4Å: Chain B: Q.10, K.112, K.193 Ligands: ATP.5, 5BX.8 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: K.219, T.223, Y.266, G.267, K.270 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.223, A:T.223, A:K.270 GOL.7: 5 residues within 4Å: Chain B: K.219, T.223, Y.266, G.267, K.270 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.223, B:T.223, B:K.270

2 x 5BX: (5S)-5-[(1R)-1-(1H-indol-3-yl)ethyl]-2-(methylamino)-1,3-oxazol-4(5H)-one(Non-covalent)

5BX.4: 18 residues within 4Å: Chain A: F.6, S.7, G.8, I.9, Q.10, V.41, H.44, T.47, Y.126, M.130, D.133, I.134, V.142, V.144, Q.148, H.151 Ligands: ATP.1, MG.2 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.6, A:F.6, A:Q.10, A:D.133, A:I.134, A:V.142, A:V.144 Hydrogen bonds: A:H.44, A:H.44, A:D.133 Water bridges: A:Q.10, A:Q.10, A:Q.148, A:Q.148 5BX.8: 18 residues within 4Å: Chain B: F.6, S.7, G.8, I.9, Q.10, V.41, H.44, T.47, Y.126, M.130, D.133, I.134, V.142, V.144, Q.148, H.151 Ligands: ATP.5, MG.6 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:F.6, B:F.6, B:Q.10, B:D.133, B:I.134, B:V.142, B:V.144 Hydrogen bonds: B:H.44, B:H.44, B:D.133, B:D.133 Water bridges: B:Q.10, B:Q.10, B:Q.148, B:Q.148

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Williams, T.L. et al., Selective Inhibition of Bacterial Tryptophanyl-tRNA Synthetases by Indolmycin Is Mechanism-based. J.Biol.Chem. (2016)

Release Date

2015-11-18

Peptides

Tryptophan--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Tryptophan--tRNA ligase