- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.44 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, 9TU.5
20 PLIP interactions:20 interactions with chain A- Hydrogen bonds: A:E.152, A:L.159, A:E.216, A:S.219, A:G.243, A:R.246
- Water bridges: A:Q.107, A:R.150, A:R.150, A:R.150, A:R.150, A:S.219
- 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, 9TU.12
21 PLIP interactions:21 interactions with chain B- Hydrogen bonds: B:E.152, B:E.152, B:L.159, B:E.216, B:S.219, B:G.243, B:R.246
- Water bridges: B:Q.107, B:R.150, B:R.150, B:R.150, B:R.150, B:S.219
- 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 9TU: N6-[({3-[3-(trifluoromethyl)-3H-diaziren-3-yl]phenyl}methoxy)carbonyl]-L-lysine(Non-covalent)
9TU.5: 21 residues within 4Å:- Chain A: M.96, M.120, A.122, P.123, A.126, L.129, R.150, M.164, N.166, C.168, F.204, S.219, I.225, L.227, D.228, W.231, I.233, W.237, G.239, G.241
- Ligands: ATP.4
11 PLIP interactions:11 interactions with chain A- Hydrophobic interactions: A:A.126, A:L.129, A:I.233
- Hydrogen bonds: A:N.166, A:N.166, A:D.228
- Water bridges: A:A.122
- Salt bridges: A:R.150
- pi-Stacking: A:W.237, A:W.237
- Halogen bonds: A:A.122
9TU.12: 21 residues within 4Å:- Chain B: M.96, M.120, A.122, P.123, A.126, L.129, R.150, M.164, N.166, C.168, F.204, S.219, I.225, L.227, D.228, W.231, I.233, W.237, G.239, G.241
- Ligands: ATP.11
10 PLIP interactions:10 interactions with chain B- Hydrophobic interactions: B:A.126, B:L.129, B:I.233
- Hydrogen bonds: B:N.166, B:N.166
- Water bridges: B:A.122
- Salt bridges: B:R.150
- pi-Stacking: B:W.237, B:W.237
- Halogen bonds: B:A.122
- 4 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.5
K.7: 3 residues within 4Å:- Chain A: E.161, R.262
- Chain B: P.85
3 PLIP interactions:2 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:E.161, A:R.262, H2O.4
K.13: 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.12, H2O.16
K.14: 3 residues within 4Å:- Chain A: P.85
- Chain B: E.161, R.262
3 PLIP interactions:2 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:E.161, B:R.262, H2O.15
- 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 1.44 Å
- Oligo State
- homo-dimer
- Ligands
- 6 x MG: MAGNESIUM ION(Non-covalent)
- 2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)
- 2 x 9TU: N6-[({3-[3-(trifluoromethyl)-3H-diaziren-3-yl]phenyl}methoxy)carbonyl]-L-lysine(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