SMTL ID : 6ly6.1

PylRS C-terminus domain mutant bound with 3-(1-Naphthyl)-L-alanine and AMPNP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

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

ANP.1: 19 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, F.245, G.246, E.248, R.249, I.260 Ligands: MG.2, MG.3, ALN.4 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:R.153, A:H.161, A:L.162, A:E.219, A:E.219, A:E.219, A:G.246, A:R.249, A:R.249 Water bridges: A:E.106, A:Q.110, A:H.161 Salt bridges: A:R.153 pi-Stacking: A:F.165, A:F.165 pi-Cation interactions: A:R.249, A:R.249 ANP.5: 19 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, F.245, G.246, E.248, R.249, I.260 Ligands: MG.6, MG.7, ALN.8 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:R.153, B:H.161, B:L.162, B:E.219, B:E.219, B:E.219, B:G.246, B:R.249, B:R.249 Water bridges: B:E.106, B:Q.110, B:H.161 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 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.219, A:S.222 MG.3: 4 residues within 4Å: Chain A: Q.110, R.153, E.155 Ligands: ANP.1 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain B: E.219, S.222 Ligands: ANP.5 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.219, B:S.222 MG.7: 4 residues within 4Å: Chain B: Q.110, R.153, E.155 Ligands: ANP.5 No protein-ligand interaction detected (PLIP)

2 x ALN: NAPHTHALEN-2-YL-3-ALANINE(Non-covalent)

ALN.4: 17 residues within 4Å: Chain A: M.123, L.124, A.125, L.128, R.153, M.167, G.169, F.170, Q.171, S.222, A.223, G.224, W.240, G.242, A.243, G.244 Ligands: ANP.1 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.128, A:W.240 Hydrogen bonds: A:L.124, A:A.125 ALN.8: 17 residues within 4Å: Chain B: M.123, L.124, A.125, L.128, R.153, M.167, G.169, F.170, Q.171, S.222, A.223, G.224, W.240, G.242, A.243, G.244 Ligands: ANP.5 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.128, 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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