SMTL ID : 2q7g.1

Pyrrolysine tRNA Synthetase bound to a pyrrolysine analogue (cyc) and ATP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: R.167 Ligands: ATP.3 No protein-ligand interaction detected (PLIP) MG.2: 3 residues within 4Å: Chain A: E.233, S.236 Ligands: ATP.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.233, A:S.236, H2O.9, H2O.10 MG.15: 2 residues within 4Å: Chain B: R.167 Ligands: ATP.17 No protein-ligand interaction detected (PLIP) MG.16: 3 residues within 4Å: Chain B: E.233, S.236 Ligands: ATP.17 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.233, B:S.236, H2O.18, H2O.20

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.3: 20 residues within 4Å: Chain A: R.167, E.169, E.174, H.175, L.176, F.179, M.181, E.233, L.234, S.235, S.236, G.258, F.259, G.260, R.263, I.274 Ligands: MG.1, MG.2, EDO.13, CCL.14 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:E.169, A:L.176, A:E.233, A:E.233, A:S.236, A:S.236, A:G.260, A:R.263 Water bridges: A:R.167, A:R.167, A:R.167, A:H.175, A:S.236 Salt bridges: A:R.167, A:R.167, A:H.175, A:R.263 pi-Stacking: A:F.179, A:F.179 pi-Cation interactions: A:R.263 ATP.17: 20 residues within 4Å: Chain B: R.167, E.169, E.174, H.175, L.176, F.179, M.181, E.233, L.234, S.235, S.236, G.258, F.259, G.260, R.263, I.274 Ligands: MG.15, MG.16, EDO.27, CCL.28 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:E.169, B:L.176, B:E.233, B:E.233, B:S.236, B:S.236, B:G.260, B:R.263 Water bridges: B:R.167, B:R.167, B:R.167, B:H.175, B:S.236 Salt bridges: B:R.167, B:R.167, B:H.175, B:R.263 pi-Stacking: B:F.179, B:F.179 pi-Cation interactions: B:R.263

20 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 8 residues within 4Å: Chain A: N.78, R.276, A.277, A.278, Y.283, Y.284, N.285, G.286 Ligand excluded by PLIP EDO.5: 7 residues within 4Å: Chain A: Y.79, K.82, L.83, E.86, L.265, K.268, H.269 Ligand excluded by PLIP EDO.6: 4 residues within 4Å: Chain A: D.210, H.229, G.230 Ligands: EDO.8 Ligand excluded by PLIP EDO.7: 1 residues within 4Å: Chain A: E.194 Ligand excluded by PLIP EDO.8: 7 residues within 4Å: Chain A: D.210, F.211, K.212, M.228, H.229, G.230 Ligands: EDO.6 Ligand excluded by PLIP EDO.9: 2 residues within 4Å: Chain A: S.62 Ligands: EDO.10 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: S.58, L.61, S.62, K.65 Ligands: EDO.9 Ligand excluded by PLIP EDO.11: 7 residues within 4Å: Chain A: R.147, D.150, M.187, G.249, I.250, D.251, K.252 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain A: L.176, E.177, E.178, A.278 Ligand excluded by PLIP EDO.13: 7 residues within 4Å: Chain A: E.174, H.175, D.231, L.232, E.233, R.263 Ligands: ATP.3 Ligand excluded by PLIP EDO.18: 8 residues within 4Å: Chain B: N.78, R.276, A.277, A.278, Y.283, Y.284, N.285, G.286 Ligand excluded by PLIP EDO.19: 7 residues within 4Å: Chain B: Y.79, K.82, L.83, E.86, L.265, K.268, H.269 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain B: D.210, H.229, G.230 Ligands: EDO.22 Ligand excluded by PLIP EDO.21: 1 residues within 4Å: Chain B: E.194 Ligand excluded by PLIP EDO.22: 7 residues within 4Å: Chain B: D.210, F.211, K.212, M.228, H.229, G.230 Ligands: EDO.20 Ligand excluded by PLIP EDO.23: 2 residues within 4Å: Chain B: S.62 Ligands: EDO.24 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain B: S.58, L.61, S.62, K.65 Ligands: EDO.23 Ligand excluded by PLIP EDO.25: 7 residues within 4Å: Chain B: R.147, D.150, M.187, G.249, I.250, D.251, K.252 Ligand excluded by PLIP EDO.26: 4 residues within 4Å: Chain B: L.176, E.177, E.178, A.278 Ligand excluded by PLIP EDO.27: 7 residues within 4Å: Chain B: E.174, H.175, D.231, L.232, E.233, R.263 Ligands: ATP.17 Ligand excluded by PLIP

2 x CCL: N~6~-[(CYCLOPENTYLOXY)CARBONYL]-D-LYSINE(Non-covalent)

CCL.14: 14 residues within 4Å: Chain A: M.137, A.139, L.142, Y.143, N.183, F.184, C.185, S.236, V.238, W.254, G.256, A.257, G.258 Ligands: ATP.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.142, A:Y.143, A:W.254 Hydrogen bonds: A:N.183 Water bridges: A:S.236 CCL.28: 14 residues within 4Å: Chain B: M.137, A.139, L.142, Y.143, N.183, F.184, C.185, S.236, V.238, W.254, G.256, A.257, G.258 Ligands: ATP.17 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.142, B:Y.143, B:W.254 Hydrogen bonds: B:N.183 Water bridges: B:S.236

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kavran, J.M. et al., Structure of pyrrolysyl-tRNA synthetase, an archaeal enzyme for genetic code innovation. Proc.Natl.Acad.Sci.Usa (2007)

Release Date

2007-07-24

Peptides

Pyrrolysyl-tRNA synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Pyrrolysyl-tRNA synthetase

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