SMTL ID : 8ke3.1

PylRS C-terminus domain mutant bound with D-3-trifluoromethylphenylalanine and AMPNP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 16 residues within 4Å: Chain A: R.153, E.155, H.161, L.162, F.165, M.167, E.219, L.220, S.221, S.222, G.244, G.246, R.249 Ligands: MG.2, MG.3, FXC.4 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:R.153, A:E.155, A:L.162, A:E.219, A:E.219, A:S.222, A:S.222, A:G.246, A:R.249, A:R.249 Water bridges: A:E.106, A:Q.110, A:Q.110 Salt bridges: A:R.153 pi-Stacking: A:F.165, A:F.165 pi-Cation interactions: A:R.249, A:R.249 ANP.5: 16 residues within 4Å: Chain B: R.153, E.155, H.161, L.162, F.165, M.167, E.219, L.220, S.221, S.222, G.244, G.246, R.249 Ligands: MG.6, MG.7, FXC.8 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:R.153, B:E.155, B:L.162, B:E.219, B:E.219, B:S.222, B:S.222, B:G.246, B:R.249, B:R.249 Water bridges: B:E.106, B:Q.110, B:Q.110 Salt bridges: B:R.153 pi-Stacking: B:F.165, B:F.165 pi-Cation interactions: B:R.249, B:R.249

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: E.219, S.222 Ligands: ANP.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.219, A:E.219, A:S.222, H2O.2 MG.3: 2 residues within 4Å: Chain A: R.153 Ligands: ANP.1 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain B: E.219, S.222 Ligands: ANP.5 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.219, B:E.219, B:S.222, H2O.7 MG.7: 2 residues within 4Å: Chain B: R.153 Ligands: ANP.5 No protein-ligand interaction detected (PLIP)

2 x FXC: (2R)-2-azanyl-3-[3-(trifluoromethyl)phenyl]propanoic acid(Non-covalent)

FXC.4: 11 residues within 4Å: Chain A: A.125, L.128, R.153, G.169, Q.171, S.222, W.240, G.242, A.243, G.244 Ligands: ANP.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.128 Hydrogen bonds: A:R.153, A:S.222, A:G.244 Water bridges: A:A.125 FXC.8: 11 residues within 4Å: Chain B: A.125, L.128, R.153, G.169, Q.171, S.222, W.240, G.242, A.243, G.244 Ligands: ANP.5 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.128 Hydrogen bonds: B:R.153, B:S.222, B:G.244 Water bridges: B:A.125

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jiang, H.K. et al., Rational design of the genetic code expansion toolkit for in vivo encoding of D-amino acids. Front Genet (2023)

Release Date

2023-11-01

Peptides

Pyrrolysine--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Pyrrolysine--tRNA ligase

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