SMTL ID : 2zim.1

Pyrrolysyl-tRNA synthetase bound to adenylated pyrrolysine and pyrophosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 9 residues within 4Å: Chain A: N.78, L.80, R.276, A.277, A.278, Y.283, Y.284, N.285, G.286 Ligand excluded by PLIP EDO.2: 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.3: 5 residues within 4Å: Chain A: R.89, F.90, D.93, R.94, H.206 Ligand excluded by PLIP EDO.4: 6 residues within 4Å: Chain A: D.210, F.211, K.212, H.229, G.230 Ligands: EDO.8 Ligand excluded by PLIP EDO.5: 6 residues within 4Å: Chain A: D.150, M.187, G.249, I.250, D.251, K.252 Ligand excluded by PLIP EDO.6: 7 residues within 4Å: Chain A: E.174, H.175, D.231, L.232, E.233, R.263 Ligands: POP.12 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: F.90, R.94, I.199, D.202 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: D.210, H.229, G.230 Ligands: EDO.4 Ligand excluded by PLIP EDO.9: 1 residues within 4Å: Chain A: E.194 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: Q.69, Q.70, A.73, E.74 Ligand excluded by PLIP EDO.13: 9 residues within 4Å: Chain B: N.78, L.80, R.276, A.277, A.278, Y.283, Y.284, N.285, G.286 Ligand excluded by PLIP EDO.14: 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.15: 5 residues within 4Å: Chain B: R.89, F.90, D.93, R.94, H.206 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain B: D.210, F.211, K.212, H.229, G.230 Ligands: EDO.20 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain B: D.150, M.187, G.249, I.250, D.251, K.252 Ligand excluded by PLIP EDO.18: 7 residues within 4Å: Chain B: E.174, H.175, D.231, L.232, E.233, R.263 Ligands: POP.24 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain B: F.90, R.94, I.199, D.202 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain B: D.210, H.229, G.230 Ligands: EDO.16 Ligand excluded by PLIP EDO.21: 1 residues within 4Å: Chain B: E.194 Ligand excluded by PLIP EDO.22: 4 residues within 4Å: Chain B: Q.69, Q.70, A.73, E.74 Ligand excluded by PLIP

2 x YLY: (2R)-2-AMINO-6-({[(2S,3R)-3-METHYLPYRROLIDIN-2-YL]CARBONYL}AMINO)HEXANOYL [(2S,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL HYDROGEN (R)-PHOSPHATE(Non-covalent)

YLY.11: 27 residues within 4Å: Chain A: M.137, A.139, L.142, Y.143, R.167, E.169, E.174, H.175, L.176, F.179, M.181, N.183, F.184, C.185, Y.221, E.233, L.234, S.235, S.236, V.238, W.254, G.256, A.257, G.258, G.260, R.263 Ligands: POP.12 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:L.142, A:Y.143, A:V.238 Hydrogen bonds: A:E.169, A:L.176, A:N.183, A:Y.221, A:Y.221, A:Y.221, A:Y.221, A:E.233, A:S.236, A:G.258, A:G.260, A:R.263 Water bridges: A:L.138, A:A.139, A:S.236, A:S.236 Salt bridges: A:R.167, A:R.167 pi-Stacking: A:F.179, A:F.179 pi-Cation interactions: A:R.263 YLY.23: 27 residues within 4Å: Chain B: M.137, A.139, L.142, Y.143, R.167, E.169, E.174, H.175, L.176, F.179, M.181, N.183, F.184, C.185, Y.221, E.233, L.234, S.235, S.236, V.238, W.254, G.256, A.257, G.258, G.260, R.263 Ligands: POP.24 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:L.142, B:Y.143, B:V.238 Hydrogen bonds: B:E.169, B:L.176, B:N.183, B:Y.221, B:Y.221, B:Y.221, B:Y.221, B:E.233, B:S.236, B:G.258, B:G.260, B:R.263 Water bridges: B:L.138, B:A.139, B:S.236, B:S.236 Salt bridges: B:R.167, B:R.167 pi-Stacking: B:F.179, B:F.179 pi-Cation interactions: B:R.263

2 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.12: 6 residues within 4Å: Chain A: R.167, H.175, E.233, R.263 Ligands: EDO.6, YLY.11 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.233 Water bridges: A:R.167 Salt bridges: A:R.167, A:H.175, A:R.263 POP.24: 6 residues within 4Å: Chain B: R.167, H.175, E.233, R.263 Ligands: EDO.18, YLY.23 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.233 Water bridges: B:R.167 Salt bridges: B:R.167, B:H.175, B:R.263

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

2008-03-04

Peptides

Pyrrolysyl-tRNA synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Pyrrolysyl-tRNA synthetase

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