- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.40 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
- Ligands: MG.1, MG.2, MG.3, 9V6.5, 9V6.6
19 PLIP interactions:19 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:E.157
- 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.15: 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
- Ligands: MG.12, MG.13, MG.14, 9V6.16, 9V6.17
21 PLIP interactions:21 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:E.157, B:E.157
- 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 9V6: (2S)-2-azanyl-6-[(2-chlorophenyl)methoxycarbonylamino]hexanoic acid(Non-covalent)
9V6.5: 20 residues within 4Å:- Chain A: M.96, M.120, A.122, A.126, L.129, R.150, M.164, N.166, C.168, C.201, F.204, S.219, D.228, I.233, W.237, G.239, A.240, G.241
- Ligands: ATP.4, 9V6.6
10 PLIP interactions:10 interactions with chain A- Hydrophobic interactions: A:A.126, A:L.129, A:F.204, A:I.233
- Hydrogen bonds: A:R.150, A:N.166
- Water bridges: A:N.166
- Salt bridges: A:R.150
- pi-Stacking: A:W.237, A:W.237
9V6.6: 21 residues within 4Å:- Chain A: M.96, A.122, L.125, A.126, L.129, M.164, N.166, C.168, F.204, S.219, V.221, L.227, D.228, W.231, I.233, W.237, G.239, A.240, G.241
- Ligands: ATP.4, 9V6.5
10 PLIP interactions:10 interactions with chain A- Hydrophobic interactions: A:A.126, A:F.204, A:L.227, A:L.227, A:W.231, A:W.231, A:I.233, A:W.237
- Hydrogen bonds: A:N.166, A:S.219
9V6.16: 20 residues within 4Å:- Chain B: M.96, M.120, A.122, A.126, L.129, R.150, M.164, N.166, C.168, C.201, F.204, S.219, D.228, I.233, W.237, G.239, A.240, G.241
- Ligands: ATP.15, 9V6.17
11 PLIP interactions:11 interactions with chain B- Hydrophobic interactions: B:A.126, B:L.129, B:F.204, B:I.233
- Hydrogen bonds: B:R.150, B:N.166
- Water bridges: B:N.166, B:S.219
- Salt bridges: B:R.150
- pi-Stacking: B:W.237, B:W.237
9V6.17: 21 residues within 4Å:- Chain B: M.96, A.122, L.125, A.126, L.129, M.164, N.166, C.168, F.204, S.219, V.221, L.227, D.228, W.231, I.233, W.237, G.239, A.240, G.241
- Ligands: ATP.15, 9V6.16
10 PLIP interactions:10 interactions with chain B- Hydrophobic interactions: B:A.126, B:F.204, B:L.227, B:L.227, B:W.231, B:W.231, B:I.233, B:W.237
- Hydrogen bonds: B:N.166, B:S.219
- 4 x K: POTASSIUM ION(Non-covalent)
K.7: 4 residues within 4Å:- Chain A: L.22, N.23, P.24, D.26
No protein-ligand interaction detected (PLIP)K.8: 3 residues within 4Å:- Chain A: E.161, R.262
- Ligands: EDO.10
2 PLIP interactions:2 interactions with chain A- Metal complexes: A:E.161, A:R.262
K.18: 4 residues within 4Å:- Chain B: L.22, N.23, P.24, D.26
No protein-ligand interaction detected (PLIP)K.19: 3 residues within 4Å:- Chain B: E.161, R.262
- Ligands: EDO.21
2 PLIP interactions:2 interactions with chain B- Metal complexes: B:E.161, B:R.262
- 6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.9: 4 residues within 4Å:- Chain A: D.16, E.19, V.20, Y.266
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:D.16, A:V.20, A:Y.266, A:Y.266
EDO.10: 6 residues within 4Å:- Chain A: D.154, L.159, E.160, E.161, K.258
- Ligands: K.8
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:D.154, A:E.160, A:E.161, A:K.258
EDO.11: 4 residues within 4Å:- Chain A: L.190, G.191, I.192, K.251
1 PLIP interactions:1 interactions with chain A- Water bridges: A:G.191
EDO.20: 4 residues within 4Å:- Chain B: D.16, E.19, V.20, Y.266
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:D.16, B:D.16, B:V.20, B:Y.266
EDO.21: 6 residues within 4Å:- Chain B: D.154, L.159, E.160, E.161, K.258
- Ligands: K.19
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:D.154, B:E.160, B:E.161, B:K.258
EDO.22: 4 residues within 4Å:- Chain B: L.190, G.191, I.192, K.251
1 PLIP interactions:1 interactions with chain B- Water bridges: B:G.191
- 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 1.40 Å
- Oligo State
- homo-dimer
- Ligands
- 6 x MG: MAGNESIUM ION(Non-covalent)
- 2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)
- 4 x 9V6: (2S)-2-azanyl-6-[(2-chlorophenyl)methoxycarbonylamino]hexanoic acid(Non-covalent)
- 4 x K: POTASSIUM ION(Non-covalent)
- 6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 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