- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.55 Å
- Oligo State
- homo-dimer
- Ligands
- 6 x MG: MAGNESIUM ION(Non-covalent)
- 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, 9U9.5
23 PLIP interactions:23 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:E.216, A:E.216, 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.12: 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.9, MG.10, MG.11, 9U9.13
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: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: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 9U9: N6-({[(1R,8S,9s)-bicyclo[6.1.0]non-4-yn-9-yl]methoxy}carbonyl)-L-lysine(Non-covalent)
9U9.5: 17 residues within 4Å:- Chain A: M.96, M.120, A.122, A.126, M.164, N.166, C.168, F.204, S.219, L.227, D.228, W.231, I.233, W.237, G.239, G.241
- Ligands: ATP.4
9 PLIP interactions:9 interactions with chain A- Hydrophobic interactions: A:A.122, A:F.204, A:L.227, A:I.233, A:W.237, A:W.237, A:W.237
- Hydrogen bonds: A:N.166
- Water bridges: A:N.166
9U9.13: 17 residues within 4Å:- Chain B: M.96, M.120, A.122, A.126, M.164, N.166, C.168, F.204, S.219, L.227, D.228, W.231, I.233, W.237, G.239, G.241
- Ligands: ATP.12
9 PLIP interactions:9 interactions with chain B- Hydrophobic interactions: B:A.122, B:F.204, B:L.227, B:I.233, B:W.237, B:W.237, B:W.237
- Hydrogen bonds: B:N.166
- Water bridges: B:N.166
- 6 x K: POTASSIUM ION(Non-covalent)
K.6: 4 residues within 4Å:- Chain A: L.22, N.23, P.24, D.26
3 PLIP interactions:1 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: A:N.23, H2O.1, H2O.6
K.7: 2 residues within 4Å:- Chain A: E.161, R.262
2 PLIP interactions:2 interactions with chain A- Metal complexes: A:E.161, A:R.262
K.8: 3 residues within 4Å:- Chain A: A.261, S.263, Y.266
3 PLIP interactions:2 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:A.261, A:Y.266, H2O.15
K.14: 4 residues within 4Å:- Chain B: L.22, N.23, P.24, D.26
3 PLIP interactions:1 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: B:N.23, H2O.13, H2O.18
K.15: 2 residues within 4Å:- Chain B: E.161, R.262
2 PLIP interactions:2 interactions with chain B- Metal complexes: B:E.161, B:R.262
K.16: 3 residues within 4Å:- Chain B: A.261, S.263, Y.266
3 PLIP interactions:2 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:A.261, B:Y.266, H2O.3
- 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 1.55 Å
- Oligo State
- homo-dimer
- Ligands
- 6 x MG: MAGNESIUM ION(Non-covalent)
- 2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)
- 2 x 9U9: N6-({[(1R,8S,9s)-bicyclo[6.1.0]non-4-yn-9-yl]methoxy}carbonyl)-L-lysine(Non-covalent)
- 6 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