SMTL ID : 6x94.1

An orthogonal seryl-tRNA synthetase/tRNA pair for noncanonical amino acid mutagenesis in Escherichia coli

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

monomer

Ligands

1 x SSA: 5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE(Non-covalent)

SSA.1: 19 residues within 4Å: Chain A: T.229, E.231, R.258, E.260, I.272, R.273, N.274, F.277, K.279, E.281, E.345, I.346, S.347, S.348, N.377, G.378, S.379, A.382, R.385 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:T.229, A:E.231, A:R.258, A:E.260, A:N.274, A:K.279, A:E.345, A:S.348, A:S.379, A:R.385 Water bridges: A:R.258, A:R.258, A:S.348 Salt bridges: A:R.258 pi-Stacking: A:F.277, A:F.277

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 1 residues within 4Å: Chain A: D.46 No protein-ligand interaction detected (PLIP) PEG.3: 4 residues within 4Å: Chain A: R.131, Y.394, V.402, E.405 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.131, A:Q.395, A:E.405 Water bridges: A:Y.394, A:E.405, A:E.405 PEG.4: 3 residues within 4Å: Chain A: N.179, D.183, Y.410 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.179 Water bridges: A:Y.410

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.5: 6 residues within 4Å: Chain A: R.21, M.23, P.105, K.212, F.325 Ligands: K.11 No protein-ligand interaction detected (PLIP)

5 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.6: 5 residues within 4Å: Chain A: L.2, E.3, F.6, N.354, R.358 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.358, A:R.358 Water bridges: A:N.354 SCN.7: 7 residues within 4Å: Chain A: T.207, G.208, Q.209, E.231, S.326, F.352, Q.356 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.209, A:Q.356 SCN.8: 1 residues within 4Å: Chain A: I.178 No protein-ligand interaction detected (PLIP) SCN.9: 3 residues within 4Å: Chain A: K.310, L.311, P.312 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.129 SCN.10: 5 residues within 4Å: Chain A: S.109, Y.292, A.328, K.329, N.351 4 PLIP interactions: 4 interactions with chain A Water bridges: A:E.110, A:N.351, A:D.353, A:D.353

1 x K: POTASSIUM ION(Non-covalent)

K.11: 3 residues within 4Å: Chain A: R.21, G.321 Ligands: DMS.5 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:R.21, A:G.321, H2O.8, H2O.9

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.12: 1 residues within 4Å: Chain A: I.19 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zambaldo, C. et al., An orthogonal seryl-tRNA synthetase/tRNA pair for noncanonical amino acid mutagenesis in Escherichia coli. Bioorg.Med.Chem. (2020)

Release Date

2020-11-04

Peptides

Serine--tRNA ligase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Serine--tRNA ligase