- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.43 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x LYS: LYSINE(Non-covalent)
- 2 x ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER(Non-covalent)
ACP.2: 21 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, MG.3, MG.4, MG.5, GOL.9
18 PLIP interactions:18 interactions with chain A- Hydrogen bonds: A:E.264, A:E.264, A:R.269, A:N.271, A:E.421, A:E.421, A:N.424, A:G.477, A:R.480, A:R.480
- Water bridges: A:R.262, A:R.262, A:R.262
- Salt bridges: A:R.262
- pi-Stacking: A:F.274, A:F.274
- pi-Cation interactions: A:R.480, A:R.480
ACP.13: 21 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.12, MG.14, MG.15, MG.16, GOL.20
20 PLIP interactions:20 interactions with chain B- Hydrogen bonds: B:E.264, B:R.269, B:N.271, B:E.380, B:E.421, B:E.421, B:E.421, B:N.424, B:G.477, B:R.480, B:R.480
- Water bridges: B:R.262, B:R.262, B:R.262, B:D.479
- Salt bridges: B:R.262
- pi-Stacking: B:F.274, B:F.274
- pi-Cation interactions: B:R.480, B:R.480
- 6 x MG: MAGNESIUM ION(Non-covalent)
MG.3: 5 residues within 4Å:- Chain A: R.412, E.414, E.421
- Ligands: ACP.2, MG.5
2 PLIP interactions:2 interactions with chain A- Metal complexes: A:E.414, A:E.421
MG.4: 3 residues within 4Å:- Chain A: E.264, H.270
- Ligands: ACP.2
No protein-ligand interaction detected (PLIP)MG.5: 3 residues within 4Å:- Chain A: E.421
- Ligands: ACP.2, MG.3
1 PLIP interactions:1 interactions with chain A- Metal complexes: A:E.421
MG.14: 5 residues within 4Å:- Chain B: R.412, E.414, E.421
- Ligands: ACP.13, MG.16
2 PLIP interactions:2 interactions with chain B- Metal complexes: B:E.414, B:E.421
MG.15: 3 residues within 4Å:- Chain B: E.264, H.270
- Ligands: ACP.13
No protein-ligand interaction detected (PLIP)MG.16: 3 residues within 4Å:- Chain B: E.421
- Ligands: ACP.13, MG.14
1 PLIP interactions:1 interactions with chain B- Metal complexes: B:E.421
- 12 x GOL: GLYCEROL(Non-functional Binders)
GOL.6: 6 residues within 4Å:- Chain A: Y.312, H.315, I.384, G.418, R.420, H.489
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:R.420, A:R.420
GOL.7: 10 residues within 4Å:- Chain A: L.190, R.194, I.257, N.258
- Chain B: R.194, E.204, E.206, I.257, N.258
- Ligands: GOL.18
8 PLIP interactions:6 interactions with chain A, 2 interactions with chain B- Hydrogen bonds: A:R.194, A:R.194, A:I.257, A:N.258, B:R.194, B:N.258
- Water bridges: A:R.259, A:R.259
GOL.8: 7 residues within 4Å:- Chain A: Y.286, T.390, E.391, N.403, T.410, D.411, R.412
7 PLIP interactions:7 interactions with chain A- Hydrogen bonds: A:Y.286, A:E.391, A:N.403, A:T.410, A:D.411, A:R.412, A:R.412
GOL.9: 8 residues within 4Å:- Chain A: A.217, S.218, V.396, R.412, N.424, F.426
- Ligands: LYS.1, ACP.2
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:S.218, A:S.218, A:N.424
GOL.10: 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
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:P.214, A:A.217, A:A.219, A:F.455
GOL.11: 1 residues within 4Å:- Chain A: K.333
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:K.333
- Water bridges: A:K.333
GOL.17: 6 residues within 4Å:- Chain B: Y.312, H.315, I.384, G.418, R.420, H.489
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:Y.312, B:R.420, B:R.420, B:H.489
GOL.18: 10 residues within 4Å:- Chain A: R.194, E.204, E.206, I.257, N.258
- Chain B: L.190, R.194, I.257, N.258
- Ligands: GOL.7
10 PLIP interactions:6 interactions with chain B, 4 interactions with chain A- Hydrogen bonds: B:R.194, B:R.194, B:I.257, B:N.258, A:R.194, A:N.258
- Water bridges: B:R.259, B:R.259, A:E.204, A:E.204
GOL.19: 7 residues within 4Å:- Chain B: Y.286, T.390, E.391, N.403, T.410, D.411, R.412
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:E.391, B:N.403, B:T.410, B:R.412, B:R.412
GOL.20: 8 residues within 4Å:- Chain B: A.217, S.218, V.396, R.412, N.424, F.426
- Ligands: LYS.12, ACP.13
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:S.218, B:S.218, B:N.424
GOL.21: 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
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:P.214, B:A.217, B:A.219, B:F.455
GOL.22: 1 residues within 4Å:- Chain B: K.333
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:K.333
- Water bridges: B:K.333
- 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 2.43 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x LYS: LYSINE(Non-covalent)
- 2 x ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER(Non-covalent)
- 6 x MG: MAGNESIUM ION(Non-covalent)
- 12 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