- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.75 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, 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, 9VC.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.12: 18 residues within 4Å:- Chain B: R.150, E.152, 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, 9VC.13
22 PLIP interactions:22 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: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
- 4 x 9VC: (2S)-2-azanyl-6-(phenylmethoxycarbonylamino)hexanoic acid(Non-covalent)
9VC.5: 15 residues within 4Å:- Chain A: M.120, A.122, A.126, L.129, M.164, N.166, C.168, F.204, S.219, D.228, W.237, G.239, G.241
- Ligands: ATP.4, 9VC.6
6 PLIP interactions:6 interactions with chain A- Hydrophobic interactions: A:A.126, A:L.129, A:W.237, A:W.237
- Hydrogen bonds: A:N.166
- Water bridges: A:N.166
9VC.6: 16 residues within 4Å:- Chain A: M.96, A.122, A.126, L.129, N.166, C.168, F.204, S.219, V.221, L.227, D.228, W.231, W.237, G.239, G.241
- Ligands: 9VC.5
10 PLIP interactions:10 interactions with chain A- Hydrophobic interactions: A:A.126, A:F.204, A:F.204, A:L.227, A:W.231, A:W.237, A:W.237
- Hydrogen bonds: A:N.166, A:S.219
- Water bridges: A:N.166
9VC.13: 15 residues within 4Å:- Chain B: M.120, A.122, A.126, L.129, M.164, N.166, C.168, F.204, S.219, D.228, W.237, G.239, G.241
- Ligands: ATP.12, 9VC.14
6 PLIP interactions:6 interactions with chain B- Hydrophobic interactions: B:A.126, B:L.129, B:W.237, B:W.237
- Hydrogen bonds: B:N.166
- Water bridges: B:N.166
9VC.14: 16 residues within 4Å:- Chain B: M.96, A.122, A.126, L.129, N.166, C.168, F.204, S.219, V.221, L.227, D.228, W.231, W.237, G.239, G.241
- Ligands: 9VC.13
10 PLIP interactions:10 interactions with chain B- Hydrophobic interactions: B:A.126, B:F.204, B:F.204, B:L.227, B:W.231, B:W.237, B:W.237
- Hydrogen bonds: B:N.166, B:S.219
- Water bridges: B:N.166
- 4 x K: POTASSIUM ION(Non-covalent)
K.7: 3 residues within 4Å:- Chain A: P.24, D.26, E.27
3 PLIP interactions:2 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:P.24, A:D.26, H2O.5
K.8: 3 residues within 4Å:- Chain A: E.161, A.261, R.262
3 PLIP interactions:2 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:E.161, A:R.262, H2O.6
K.15: 3 residues within 4Å:- Chain B: P.24, D.26, E.27
3 PLIP interactions:2 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:P.24, B:D.26, H2O.13
K.16: 3 residues within 4Å:- Chain B: E.161, A.261, R.262
3 PLIP interactions:2 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:E.161, B:R.262, H2O.14
- 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 1.75 Å
- Oligo State
- homo-dimer
- Ligands
- 6 x MG: MAGNESIUM ION(Non-covalent)
- 2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)
- 4 x 9VC: (2S)-2-azanyl-6-(phenylmethoxycarbonylamino)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