SMTL ID : 5k1p.1

Catalytic domain of polyspecific pyrrolysyl-tRNA synthetase mutant N346A/C348A in complex with AMPPNP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

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

ANP.1: 19 residues within 4Å: Chain A: R.144, E.146, H.152, L.153, E.154, F.156, M.158, E.210, L.211, S.212, S.213, G.235, F.236, G.237, E.239, R.240, I.251 Ligands: MG.2, MG.3 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:R.144, A:E.146, A:H.152, A:L.153, A:E.210, A:E.210, A:E.210, A:L.211, A:G.237, A:R.240, A:R.240, A:R.240 Salt bridges: A:R.144 pi-Stacking: A:F.156, A:F.156 pi-Cation interactions: A:R.240 ANP.4: 19 residues within 4Å: Chain B: R.144, E.146, H.152, L.153, E.154, F.156, M.158, E.210, L.211, S.212, S.213, G.235, F.236, G.237, E.239, R.240, I.251 Ligands: MG.5, MG.6 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:R.144, B:E.146, B:E.146, B:H.152, B:L.153, B:E.210, B:E.210, B:L.211, B:G.237, B:R.240, B:R.240, B:R.240 Salt bridges: B:R.144 pi-Stacking: B:F.156, B:F.156 pi-Cation interactions: B:R.240

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: E.210, S.213 Ligands: ANP.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.210, A:E.210, A:S.213, H2O.2, H2O.8 MG.3: 4 residues within 4Å: Chain A: Q.101, R.144, H.152 Ligands: ANP.1 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain B: E.210, S.213 Ligands: ANP.4 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.210, B:E.210, B:S.213, H2O.13, H2O.18 MG.6: 4 residues within 4Å: Chain B: Q.101, R.144, H.152 Ligands: ANP.4 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, Y.J. et al., Genetically encoded fluorophenylalanines enable insights into the recognition of lysine trimethylation by an epigenetic reader. Chem.Commun.(Camb.) (2016)

Release Date

2016-10-19

Peptides

Pyrrolysine--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Pyrrolysine--tRNA ligase