SMTL ID : 4ch3.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.28 Å

Oligo State

monomer

Ligands

1 x YLB: 5'-O-({[(2R)-2-amino-6-(butanoylamino)hexanoyl]oxy}phosphinato)adenosine(Non-covalent)

YLB.1: 26 residues within 4Å: Chain A: M.137, A.139, Y.143, R.167, E.169, E.174, H.175, L.176, F.179, M.181, N.183, F.184, C.185, E.233, L.234, S.235, S.236, V.238, W.254, G.256, A.257, G.258, F.259, G.260, R.263 Ligands: MG.2 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:A.139, A:Y.143, A:W.254 Hydrogen bonds: A:E.169, A:E.169, A:L.176, A:E.233, A:E.233, A:E.233, A:S.236, A:S.236, A:G.260 Water bridges: A:N.183 Salt bridges: A:R.167, A:R.167 pi-Stacking: A:F.179, A:F.179 pi-Cation interactions: A:R.263

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: E.233 Ligands: YLB.1 No protein-ligand interaction detected (PLIP)

5 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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.86, A:K.268, A:H.269 EDO.4: 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.5: 6 residues within 4Å: Chain A: D.150, M.187, G.249, I.250, D.251, K.252 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.251, A:D.251, A:D.251 Water bridges: A:R.147 EDO.6: 4 residues within 4Å: Chain A: Y.109, N.144, R.147, K.148 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.144, A:R.147, A:K.148 Water bridges: A:R.147 EDO.7: 6 residues within 4Å: Chain A: D.210, F.211, K.212, M.228, H.229, G.230 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.210, A:K.212, A:K.212, A:G.230

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: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

PYRROLYSINE--TRNA LIGASE

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