SMTL ID : 7u0r.1

Crystal structure of Methanomethylophilus alvus PylRS(N166A/V168A) complexed with meta-trifluoromethyl-2-benzylmalonate and AMP-PNP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x LE0: {[3-(trifluoromethyl)phenyl]methyl}propanedioic acid(Non-covalent)

LE0.1: 17 residues within 4Å: Chain A: M.123, L.124, A.125, L.128, R.153, M.167, A.169, L.170, A.171, Y.209, S.224, A.226, W.242, G.244, A.245, G.246 Ligands: ANP.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.209, A:A.226, A:W.242 Hydrogen bonds: A:L.124, A:A.125 Salt bridges: A:R.153 Halogen bonds: A:L.170 LE0.7: 14 residues within 4Å: Chain B: M.123, L.124, A.125, M.167, A.169, L.170, A.171, Y.209, S.224, W.242, G.244, A.245, G.246 Ligands: ANP.8 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Y.209, B:Y.209 Hydrogen bonds: B:L.124, B:A.125, B:Y.209, B:Y.209

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

ANP.2: 18 residues within 4Å: Chain A: R.153, E.155, M.160, H.161, L.162, F.165, M.167, E.221, V.222, C.223, S.224, G.246, G.248, R.251 Ligands: LE0.1, MG.4, MG.5, MG.6 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:R.153, A:E.155, A:E.155, A:L.162, A:E.221, A:E.221, A:C.223, A:G.248, A:R.251, A:R.251 Water bridges: A:S.224 Salt bridges: A:R.153 pi-Stacking: A:F.165, A:F.165 pi-Cation interactions: A:R.251, A:R.251 ANP.8: 17 residues within 4Å: Chain B: R.153, E.155, M.160, H.161, L.162, F.165, M.167, E.221, V.222, C.223, S.224, G.246, G.248, R.251 Ligands: LE0.7, MG.9, MG.10 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:R.153, B:E.155, B:H.161, B:L.162, B:E.221, B:E.221, B:G.246, B:G.248, B:R.251, B:R.251 Water bridges: B:Q.220 Salt bridges: B:R.153 pi-Stacking: B:F.165, B:F.165 pi-Cation interactions: B:R.251, B:R.251

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

TRS.3: 6 residues within 4Å: Chain A: I.101, L.107, Q.110, V.111, P.122, R.153 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.107, A:Q.110, A:R.153 Water bridges: A:Q.110, A:Q.110

5 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 5 residues within 4Å: Chain A: D.214, E.221, S.224 Ligands: ANP.2, MG.6 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.221, A:S.224, H2O.2, H2O.5 MG.5: 3 residues within 4Å: Chain A: R.153, H.161 Ligands: ANP.2 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain A: E.221 Ligands: ANP.2, MG.4 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.221, H2O.2, H2O.8 MG.9: 3 residues within 4Å: Chain B: R.153, E.155 Ligands: ANP.8 No protein-ligand interaction detected (PLIP) MG.10: 4 residues within 4Å: Chain B: D.214, E.221, S.224 Ligands: ANP.8 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.221, B:S.224, H2O.10

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fricke, R. et al., Expanding the substrate scope of pyrrolysyl-transfer RNA synthetase enzymes to include non-alpha-amino acids in vitro and in vivo. Nat.Chem. (2023)

Release Date

2023-06-14

Peptides

Pyrrolysyl-tRNA synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Pyrrolysyl-tRNA synthetase