SMTL ID : 1e1t.1

LYSYL-TRNA SYNTHETASE (LYSU) HEXAGONAL FORM COMPLEXED WITH THE LYSYL_ADENYLATE INTERMEDIATE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x LAD: ADENOSINE-5'-[LYSYL-PHOSPHATE](Non-covalent)

LAD.1: 27 residues within 4Å: Chain A: G.216, A.217, A.238, E.240, R.262, E.264, R.269, H.270, N.271, F.274, M.276, E.278, Y.280, E.421, I.422, G.423, N.424, F.426, E.428, G.473, L.474, G.475, G.477, R.480, I.491 Ligands: POP.2, MG.3 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:F.426 Hydrogen bonds: A:E.240, A:E.264, A:E.264, A:N.271, A:E.278, A:E.278, A:Y.280, A:N.424, A:E.428, A:G.477, A:R.480 Water bridges: A:R.262 Salt bridges: A:R.262, A:R.262 pi-Stacking: A:F.274, A:F.274 pi-Cation interactions: A:R.480, A:R.480 LAD.12: 27 residues within 4Å: Chain B: G.216, A.217, A.238, E.240, R.262, E.264, R.269, H.270, N.271, F.274, M.276, E.278, Y.280, E.421, I.422, G.423, N.424, F.426, E.428, G.473, L.474, G.475, G.477, R.480, I.491 Ligands: POP.13, MG.14 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:F.426 Hydrogen bonds: B:E.264, B:N.271, B:E.278, B:E.421, B:N.424, B:E.428, B:G.477, B:R.480 Water bridges: B:R.262, B:D.479 Salt bridges: B:R.262, B:R.262 pi-Stacking: B:F.274, B:F.274 pi-Cation interactions: B:R.480, B:R.480

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
A

B
A

LYSYL-TRNA SYNTHETASE, HEAT INDUCIBLE

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