SMTL ID : 4ch5.1

Structure of pyrrolysyl-tRNA synthetase in complex with adenylated propionyl lysine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x YLP: (S)-2-amino-6-propionamidohexanoic(((2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl)methyl phosphoric) anhydride(Non-covalent)

YLP.1: 22 residues within 4Å: Chain A: A.139, R.167, E.169, H.175, L.176, F.179, M.181, N.183, C.185, E.233, L.234, S.235, S.236, V.238, W.254, G.256, A.257, G.258, G.260, R.263 Ligands: MG.2, POP.8 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:A.139, A:V.238, A:W.254 Hydrogen bonds: A:E.169, A:E.169, A:L.176, A:N.183, A:N.183, A:E.233, A:E.233, A:S.236, A:S.236, A:G.260, A:R.263 Water bridges: A:L.138 Salt bridges: A:R.167, A:R.167 pi-Stacking: A:F.179, A:F.179 pi-Cation interactions: A:R.263 YLP.9: 22 residues within 4Å: Chain B: A.139, R.167, E.169, H.175, L.176, F.179, M.181, N.183, C.185, E.233, L.234, S.235, S.236, V.238, W.254, G.256, A.257, G.258, G.260, R.263 Ligands: MG.10, POP.16 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:A.139, B:V.238, B:W.254 Hydrogen bonds: B:E.169, B:E.169, B:L.176, B:N.183, B:N.183, B:E.233, B:E.233, B:S.236, B:S.236, B:G.260, B:R.263 Water bridges: B:L.138 Salt bridges: B:R.167, B:R.167 pi-Stacking: B:F.179, B:F.179 pi-Cation interactions: B:R.263

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: E.233, S.236 Ligands: YLP.1, POP.8 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.233 MG.10: 4 residues within 4Å: Chain B: E.233, S.236 Ligands: YLP.9, POP.16 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.233

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

EDO.3: 7 residues within 4Å: Chain A: Y.79, K.82, L.83, E.86, L.265, K.268, H.269 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.86, A:K.268, A:H.269 Water bridges: A:K.82 EDO.4: 6 residues within 4Å: Chain A: D.150, M.187, G.249, I.250, D.251, K.252 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.251 Water bridges: A:D.150 EDO.5: 8 residues within 4Å: Chain A: N.78, R.276, A.277, A.278, Y.283, Y.284, N.285, G.286 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.78, A:N.78, A:R.276, A:N.285, A:G.286 EDO.6: 5 residues within 4Å: Chain A: Y.109, N.144, R.147, K.148 Chain B: E.281 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.144, A:R.147, A:K.148 EDO.7: 6 residues within 4Å: Chain A: D.210, F.211, K.212, M.228, H.229, G.230 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.210, A:G.230, A:G.230 EDO.11: 7 residues within 4Å: Chain B: Y.79, K.82, L.83, E.86, L.265, K.268, H.269 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.86, B:K.268, B:H.269 Water bridges: B:K.82 EDO.12: 6 residues within 4Å: Chain B: D.150, M.187, G.249, I.250, D.251, K.252 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.251 Water bridges: B:D.150 EDO.13: 8 residues within 4Å: Chain B: N.78, R.276, A.277, A.278, Y.283, Y.284, N.285, G.286 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.78, B:N.78, B:R.276, B:N.285, B:G.286 EDO.14: 5 residues within 4Å: Chain A: E.281 Chain B: Y.109, N.144, R.147, K.148 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.144, B:R.147, B:K.148 EDO.15: 6 residues within 4Å: Chain B: D.210, F.211, K.212, M.228, H.229, G.230 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.210, B:G.230, B:G.230

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

POP.8: 7 residues within 4Å: Chain A: R.167, E.169, H.175, E.233, R.263 Ligands: YLP.1, MG.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.233 Salt bridges: A:R.167, A:H.175, A:H.175, A:R.263 POP.16: 7 residues within 4Å: Chain B: R.167, E.169, H.175, E.233, R.263 Ligands: YLP.9, MG.10 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.233 Salt bridges: B:R.167, B:H.175, B:H.175, B:R.263

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Flugel, V. et al., Structural Basis for the Site-Specific Incorporation of Lysine Derivatives Into Proteins. Plos One (2014)

Release Date

2014-03-19

Peptides

PYRROLYSINE--TRNA LIGASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

PYRROLYSINE--TRNA LIGASE

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