- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.35 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x LYS: LYSINE(Non-covalent)
- 2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)
ATP.2: 20 residues within 4Å:- Chain A: R.262, E.264, R.269, H.270, N.271, F.274, M.276, E.380, E.414, E.421, I.422, G.423, N.424, G.477, R.480, I.491
- Ligands: LYS.1, MN.3, MN.4, MN.5
18 PLIP interactions:18 interactions with chain A- Hydrogen bonds: A:R.262, A:E.264, A:E.264, A:R.269, A:N.271, A:E.421, A:E.421, A:N.424, A:G.477
- Water bridges: A:R.269, A:R.480
- Salt bridges: A:R.262, A:H.270, A:R.480
- pi-Stacking: A:F.274, A:F.274
- pi-Cation interactions: A:R.480, A:R.480
ATP.9: 20 residues within 4Å:- Chain B: R.262, E.264, R.269, H.270, N.271, F.274, M.276, E.380, E.414, E.421, I.422, G.423, N.424, G.477, R.480, I.491
- Ligands: LYS.8, MN.10, MN.11, MN.12
18 PLIP interactions:18 interactions with chain B- Hydrogen bonds: B:R.262, B:E.264, B:R.269, B:N.271, B:E.421, B:E.421, B:N.424, B:G.477
- Water bridges: B:R.269, B:D.479, B:R.480
- Salt bridges: B:R.262, B:H.270, B:R.480
- pi-Stacking: B:F.274, B:F.274
- pi-Cation interactions: B:R.480, B:R.480
- 6 x MN: MANGANESE (II) ION(Non-covalent)
MN.3: 4 residues within 4Å:- Chain A: E.414, E.421
- Ligands: ATP.2, MN.5
2 PLIP interactions:2 interactions with chain A- Metal complexes: A:E.414, A:E.421
MN.4: 2 residues within 4Å:- Chain A: H.270
- Ligands: ATP.2
No protein-ligand interaction detected (PLIP)MN.5: 4 residues within 4Å:- Chain A: E.380, E.421
- Ligands: ATP.2, MN.3
1 PLIP interactions:1 interactions with chain A- Metal complexes: A:E.421
MN.10: 4 residues within 4Å:- Chain B: E.414, E.421
- Ligands: ATP.9, MN.12
2 PLIP interactions:2 interactions with chain B- Metal complexes: B:E.414, B:E.421
MN.11: 2 residues within 4Å:- Chain B: H.270
- Ligands: ATP.9
No protein-ligand interaction detected (PLIP)MN.12: 4 residues within 4Å:- Chain B: E.380, E.421
- Ligands: ATP.9, MN.10
1 PLIP interactions:1 interactions with chain B- Metal complexes: B:E.421
- 4 x GOL: GLYCEROL(Non-functional Binders)
GOL.6: 9 residues within 4Å:- Chain A: L.190, R.194, I.257, N.258
- Chain B: R.194, E.204, E.206, N.258
- Ligands: GOL.13
6 PLIP interactions:4 interactions with chain A, 2 interactions with chain B- Hydrogen bonds: A:R.194, A:R.194, A:N.258, B:R.194, B:N.258
- Water bridges: A:R.259
GOL.7: 13 residues within 4Å:- Chain A: P.214, G.215, A.217, S.218, A.219, P.221, I.237, K.446, D.451, E.452, A.453, M.454, F.455
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:P.214, A:A.217, A:A.219, A:K.446, A:F.455
- Water bridges: A:K.446
GOL.13: 9 residues within 4Å:- Chain A: R.194, E.204, E.206, N.258
- Chain B: L.190, R.194, I.257, N.258
- Ligands: GOL.6
9 PLIP interactions:5 interactions with chain A, 4 interactions with chain B- Hydrogen bonds: A:R.194, A:E.206, A:N.258, B:R.194, B:R.194, B:N.258
- Water bridges: A:E.204, A:E.204, B:R.259
GOL.14: 13 residues within 4Å:- Chain B: P.214, G.215, A.217, S.218, A.219, P.221, I.237, K.446, D.451, E.452, A.453, M.454, F.455
6 PLIP interactions:6 interactions with chain B- Hydrogen bonds: B:P.214, B:A.217, B:A.219, B:K.446, B:F.455
- Water bridges: B:K.446
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Desogus, G. et al., Active Site of Lysyl-tRNA Synthetase: Structural Studies of the Adenylation Reaction. Biochemistry (2000)
- Release Date
- 2000-07-28
- Peptides
- LYSYL-TRNA SYNTHETASE: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.35 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x LYS: LYSINE(Non-covalent)
- 2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)
- 6 x MN: MANGANESE (II) ION(Non-covalent)
- 4 x GOL: GLYCEROL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Desogus, G. et al., Active Site of Lysyl-tRNA Synthetase: Structural Studies of the Adenylation Reaction. Biochemistry (2000)
- Release Date
- 2000-07-28
- Peptides
- LYSYL-TRNA SYNTHETASE: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
A