- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.40 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x LAD: ADENOSINE-5'-[LYSYL-PHOSPHATE](Non-covalent)
- 2 x POP: PYROPHOSPHATE 2-(Non-covalent)
POP.2: 7 residues within 4Å:- Chain A: R.262, H.270, E.421, R.480
- Ligands: LAD.1, MG.3, MG.4
7 PLIP interactions:7 interactions with chain A- Hydrogen bonds: A:R.262, A:R.269, A:E.421
- Water bridges: A:R.269, A:R.480
- Salt bridges: A:H.270, A:R.480
POP.13: 7 residues within 4Å:- Chain B: R.262, H.270, E.421, R.480
- Ligands: LAD.12, MG.14, MG.15
7 PLIP interactions:7 interactions with chain B- Hydrogen bonds: B:R.262, B:R.269, B:E.421
- Water bridges: B:R.269, B:R.480
- Salt bridges: B:H.270, B:R.480
- 4 x MG: MAGNESIUM ION(Non-covalent)
MG.3: 5 residues within 4Å:- Chain A: R.412, E.414, E.421
- Ligands: LAD.1, POP.2
2 PLIP interactions:2 interactions with chain A- Metal complexes: A:E.414, A:E.421
MG.4: 2 residues within 4Å:- Chain A: H.270
- Ligands: POP.2
2 PLIP interactions:1 Ligand-Water interactions, 1 Ligand-Ligand interactions- Metal complexes: H2O.2, POP.2
MG.14: 5 residues within 4Å:- Chain B: R.412, E.414, E.421
- Ligands: LAD.12, POP.13
2 PLIP interactions:2 interactions with chain B- Metal complexes: B:E.414, B:E.421
MG.15: 2 residues within 4Å:- Chain B: H.270
- Ligands: POP.13
2 PLIP interactions:1 Ligand-Ligand interactions, 1 Ligand-Water interactions- Metal complexes: POP.13, H2O.15
- 14 x GOL: GLYCEROL(Non-functional Binders)
GOL.5: 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.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.17
7 PLIP interactions:4 interactions with chain A, 3 interactions with chain B- Hydrogen bonds: A:R.194, A:R.194, A:N.258, B:R.194, B:I.257, B:N.258
- Water bridges: A:R.259
GOL.7: 8 residues within 4Å:- Chain A: Y.286, T.390, E.391, N.403, I.409, T.410, D.411, R.412
7 PLIP interactions:7 interactions with chain A- Hydrogen bonds: A:Y.286, A:E.391, A:E.391, A:N.403, A:D.411, A:R.412, A:R.412
GOL.8: 11 residues within 4Å:- Chain A: A.217, S.218, V.396, S.397, P.398, L.399, A.400, R.412, N.424, F.426, M.454
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:S.218, A:S.218, A:L.399, A:A.400, A:N.424
GOL.9: 3 residues within 4Å:- Chain A: H.315, I.384, Q.385
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:H.315, A:Q.385, A:Q.385
- Water bridges: A:V.316, A:H.382, A:I.384
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
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:P.214, A:A.217, A:A.219, A:K.446, 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, A:K.333
GOL.16: 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.17: 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
10 PLIP interactions:6 interactions with chain A, 4 interactions with chain B- Hydrogen bonds: A:R.194, A:E.206, A:I.257, A:N.258, B:R.194, B:R.194, B:N.258
- Water bridges: A:E.204, A:E.204, B:R.259
GOL.18: 8 residues within 4Å:- Chain B: Y.286, T.390, E.391, N.403, I.409, T.410, D.411, R.412
7 PLIP interactions:7 interactions with chain B- Hydrogen bonds: B:E.391, B:E.391, B:E.391, B:N.403, B:D.411, B:R.412, B:R.412
GOL.19: 11 residues within 4Å:- Chain B: A.217, S.218, V.396, S.397, P.398, L.399, A.400, R.412, N.424, F.426, M.454
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:S.218, B:S.218, B:L.399, B:A.400, B:N.424
GOL.20: 3 residues within 4Å:- Chain B: H.315, I.384, Q.385
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:Q.385, B:Q.385
- Water bridges: B:V.316, B:H.382, B:I.384
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
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:P.214, B:A.217, B:A.219, B:K.446, 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, 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, HEAT INDUCIBLE: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.40 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x LAD: ADENOSINE-5'-[LYSYL-PHOSPHATE](Non-covalent)
- 2 x POP: PYROPHOSPHATE 2-(Non-covalent)
- 4 x MG: MAGNESIUM ION(Non-covalent)
- 14 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, HEAT INDUCIBLE: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
A