- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.37 Å
- Oligo State
- homo-dimer
- Ligands
- 6 x MG: MAGNESIUM ION(Non-covalent)
- 2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)
ATP.4: 18 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
- Ligands: MG.1, MG.2, MG.3, 9VR.5
20 PLIP interactions:20 interactions with chain A- Hydrogen bonds: A:E.152, A:E.152, A:L.159, A:E.216, 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
- 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.11: 18 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
- Ligands: MG.8, MG.9, MG.10, 9VR.12
20 PLIP interactions:20 interactions with chain B- Hydrogen bonds: 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:E.216, B:E.216
- 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 9VR: (2S)-2-azanyl-6-[[4-[3-(trifluoromethyl)-1,2-diazirin-3-yl]phenyl]methoxycarbonylamino]hexanoic acid(Non-covalent)
9VR.5: 20 residues within 4Å:- Chain A: M.96, M.120, A.122, A.126, L.129, M.164, N.166, F.167, C.168, F.204, S.219, I.225, L.227, D.228, W.231, W.237, G.239, A.240, G.241
- Ligands: ATP.4
7 PLIP interactions:7 interactions with chain A- Hydrophobic interactions: A:A.122, A:A.126, A:F.204, A:F.204
- Hydrogen bonds: A:N.166
- Water bridges: A:N.166
- pi-Stacking: A:W.237
9VR.12: 20 residues within 4Å:- Chain B: M.96, M.120, A.122, A.126, L.129, M.164, N.166, F.167, C.168, F.204, S.219, I.225, L.227, D.228, W.231, W.237, G.239, A.240, G.241
- Ligands: ATP.11
8 PLIP interactions:8 interactions with chain B- Hydrophobic interactions: B:A.122, B:A.126, B:F.204, B:F.204
- Hydrogen bonds: B:N.166, B:D.228
- Water bridges: B:N.166
- pi-Stacking: B:W.237
- 4 x K: POTASSIUM ION(Non-covalent)
K.6: 2 residues within 4Å:- Chain A: P.24, D.26
5 PLIP interactions:2 interactions with chain A, 3 Ligand-Water interactions- Metal complexes: A:P.24, A:D.26, H2O.5, H2O.11, H2O.11
K.7: 4 residues within 4Å:- Chain A: L.187, N.188, I.192, D.193
3 PLIP interactions:1 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: A:I.192, H2O.1, H2O.9
K.13: 2 residues within 4Å:- Chain B: P.24, D.26
5 PLIP interactions:2 interactions with chain B, 3 Ligand-Water interactions- Metal complexes: B:P.24, B:D.26, H2O.17, H2O.23, H2O.23
K.14: 4 residues within 4Å:- Chain B: L.187, N.188, I.192, D.193
3 PLIP interactions:1 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: B:I.192, H2O.14, H2O.22
- 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
AB
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.37 Å
- Oligo State
- homo-dimer
- Ligands
- 6 x MG: MAGNESIUM ION(Non-covalent)
- 2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)
- 2 x 9VR: (2S)-2-azanyl-6-[[4-[3-(trifluoromethyl)-1,2-diazirin-3-yl]phenyl]methoxycarbonylamino]hexanoic acid(Non-covalent)
- 4 x K: POTASSIUM ION(Non-covalent)
- 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
AB
A