SMTL ID : 6ly3.1

PylRS C-terminus domain mutant bound with 3-Benzothienyl-L-alanine 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: 20 residues within 4Å: Chain A: R.153, E.155, H.161, L.162, E.163, F.165, M.167, E.219, L.220, S.221, S.222, G.244, F.245, G.246, E.248, R.249, I.260 Ligands: MG.2, MG.3, 4OG.4 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:R.153, A:H.161, A:L.162, A:L.162, A:E.219, A:E.219, A:E.219, A:S.222, A:G.246, A:R.249, A:R.249 Water bridges: A:Q.110, A:H.161, A:S.222 Salt bridges: A:R.153 pi-Stacking: A:F.165, A:F.165 pi-Cation interactions: A:R.249, A:R.249 ANP.5: 20 residues within 4Å: Chain B: R.153, E.155, H.161, L.162, E.163, F.165, M.167, E.219, L.220, S.221, S.222, G.244, F.245, G.246, E.248, R.249, I.260 Ligands: MG.6, MG.7, 4OG.8 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:R.153, B:H.161, B:L.162, B:L.162, B:E.219, B:E.219, B:E.219, B:S.222, B:G.246, B:R.249, B:R.249 Water bridges: B:Q.110, B:H.161, B:S.222 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: Q.110, R.153 Ligands: ANP.1 No protein-ligand interaction detected (PLIP) MG.3: 3 residues within 4Å: Chain A: E.219, S.222 Ligands: ANP.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.219, A:E.219, A:S.222, H2O.4, H2O.6 MG.6: 3 residues within 4Å: Chain B: Q.110, R.153 Ligands: ANP.5 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain B: E.219, S.222 Ligands: ANP.5 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.219, B:E.219, B:S.222, H2O.11, H2O.12

2 x 4OG: 3-(1-benzothiophen-3-yl)-L-alanine(Non-covalent)

4OG.4: 14 residues within 4Å: Chain A: M.123, L.124, A.125, L.128, M.167, G.169, S.222, A.223, G.224, W.240, G.242, A.243, G.244 Ligands: ANP.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.240 Hydrogen bonds: A:L.124, A:A.125 4OG.8: 14 residues within 4Å: Chain B: M.123, L.124, A.125, L.128, M.167, G.169, S.222, A.223, G.224, W.240, G.242, A.243, G.244 Ligands: ANP.5 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.240 Hydrogen bonds: B:L.124, B:A.125

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jiang, H.K. et al., Probing the Active Site of Deubiquitinase USP30 with Noncanonical Tryptophan Analogues. Biochemistry (2020)

Release Date

2020-07-08

Peptides

Pyrrolysine--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Pyrrolysine--tRNA ligase

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