SMTL ID : 6lya.1

PylRS C-terminus domain mutant bound with 1-Methyl-L-tryptophan and AMPNP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.59 Å

Oligo State

homo-dimer

Ligands

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

ANP.1: 18 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, I.260 Ligands: MG.2, MG.3, EXL.4, EDO.6 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:R.153, A:E.155, 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: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.8: 18 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, I.260 Ligands: MG.9, MG.10, EXL.11, EDO.13 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:R.153, B:E.155, 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: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: 2 residues within 4Å: Chain A: 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.7, H2O.7 MG.9: 2 residues within 4Å: Chain B: R.153 Ligands: ANP.8 No protein-ligand interaction detected (PLIP) MG.10: 3 residues within 4Å: Chain B: E.219, S.222 Ligands: ANP.8 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.219, B:E.219, B:S.222, H2O.16, H2O.17

2 x EXL: 1-Methyl-L-tryptophan(Non-covalent)

EXL.4: 14 residues within 4Å: Chain A: M.123, L.124, A.125, L.128, M.167, F.170, 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 EXL.11: 14 residues within 4Å: Chain B: M.123, L.124, A.125, L.128, M.167, F.170, S.222, A.223, G.224, W.240, G.242, A.243, G.244 Ligands: ANP.8 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.240 Hydrogen bonds: B:L.124, B:A.125

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 4 residues within 4Å: Chain A: R.75, F.76, D.79, H.192 2 PLIP interactions: 2 interactions with chain A Water bridges: A:F.76, A:H.192 EDO.6: 6 residues within 4Å: Chain A: H.161, D.217, L.218, E.219, R.249 Ligands: ANP.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.161, A:D.217, A:E.219, A:R.249, A:R.249 EDO.7: 6 residues within 4Å: Chain A: Y.65, L.69, E.72, L.251, K.254, H.255 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.72, A:K.254, A:H.255 EDO.12: 4 residues within 4Å: Chain B: R.75, F.76, D.79, H.192 2 PLIP interactions: 2 interactions with chain B Water bridges: B:F.76, B:H.192 EDO.13: 6 residues within 4Å: Chain B: H.161, D.217, L.218, E.219, R.249 Ligands: ANP.8 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.161, B:D.217, B:E.219, B:R.249, B:R.249 EDO.14: 6 residues within 4Å: Chain B: Y.65, L.69, E.72, L.251, K.254, H.255 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.72, B:K.254, B:H.255

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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