SMTL ID : 6abk.1

Crystal structure of Methanosarcina mazei PylRS(Y306A/Y384F) complexed with TeocLys

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.58 Å

Oligo State

homo-dimer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: R.150 Ligands: ATP.4 No protein-ligand interaction detected (PLIP) MG.2: 4 residues within 4Å: Chain A: E.216, S.219 Ligands: MG.3, ATP.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.216, A:S.219, H2O.3, H2O.7 MG.3: 3 residues within 4Å: Chain A: E.216 Ligands: MG.2, ATP.4 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.216, H2O.3, H2O.8 MG.6: 2 residues within 4Å: Chain B: R.150 Ligands: ATP.9 No protein-ligand interaction detected (PLIP) MG.7: 4 residues within 4Å: Chain B: E.216, S.219 Ligands: MG.8, ATP.9 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.216, B:S.219, H2O.14, H2O.18 MG.8: 3 residues within 4Å: Chain B: E.216 Ligands: MG.7, ATP.9 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.216, H2O.14, H2O.19

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.4: 19 residues within 4Å: Chain A: R.150, E.152, E.157, H.158, L.159, F.162, M.164, E.216, L.217, S.218, S.219, G.241, G.243, R.246, I.257 Ligands: MG.1, MG.2, MG.3, 9VF.5 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:E.152, A:L.159, A:E.216, A:E.216, A:S.219, A:G.243, A:R.246 Water bridges: A:R.150, A:R.150, A:R.150, A:R.150, A:H.158, A:R.246 Salt bridges: A:R.150, A:R.150, A:H.158, A:R.246 pi-Stacking: A:F.162, A:F.162 pi-Cation interactions: A:R.246, A:R.246 ATP.9: 19 residues within 4Å: Chain B: R.150, E.152, E.157, H.158, L.159, F.162, M.164, E.216, L.217, S.218, S.219, G.241, G.243, R.246, I.257 Ligands: MG.6, MG.7, MG.8, 9VF.10 23 PLIP interactions: 23 interactions with chain B Hydrogen bonds: B:E.152, B:E.152, B:L.159, B:E.216, B:E.216, B:S.219, B:G.243, B:R.246 Water bridges: B:R.150, B:R.150, B:R.150, B:R.150, B:D.154, B:H.158, B:R.246 Salt bridges: B:R.150, B:R.150, B:H.158, B:R.246 pi-Stacking: B:F.162, B:F.162 pi-Cation interactions: B:R.246, B:R.246

2 x 9VF: (2S)-2-azanyl-6-(trimethylsilylmethoxycarbonylamino)hexanoic acid(Non-covalent)

9VF.5: 15 residues within 4Å: Chain A: M.120, A.122, L.125, A.126, L.129, N.166, C.168, C.201, F.204, S.219, I.233, W.237, G.239, G.241 Ligands: ATP.4 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.204, A:F.204 Hydrogen bonds: A:N.166 Water bridges: A:A.122 9VF.10: 15 residues within 4Å: Chain B: M.120, A.122, L.125, A.126, L.129, N.166, C.168, C.201, F.204, S.219, I.233, W.237, G.239, G.241 Ligands: ATP.9 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.204, B:F.204 Hydrogen bonds: B:N.166 Water bridges: B:A.122

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yanagisawa, T. et al., Structural Basis for Genetic-Code Expansion with Bulky Lysine Derivatives by an Engineered Pyrrolysyl-tRNA Synthetase. Cell Chem Biol (2019)

Release Date

2019-04-17

Peptides

Pyrrolysine--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Pyrrolysine--tRNA ligase

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