SMTL ID : 2zio.1

Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase in complex with AlocLys-AMP and PNP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.06 Å

Oligo State

homo-dimer

Ligands

2 x 2PN: IMIDODIPHOSPHORIC ACID(Non-covalent)

2PN.1: 4 residues within 4Å: Chain A: H.175, L.232, E.233, R.263 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.175, A:E.233, A:E.233, A:R.263, A:R.263 2PN.3: 4 residues within 4Å: Chain B: H.175, L.232, E.233, R.263 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.175, B:E.233, B:E.233, B:R.263, B:R.263

2 x AYB: 5'-O-[(S)-({(2S)-2-amino-6-[(propoxycarbonyl)amino]hexanoyl}oxy)(hydroxy)phosphoryl]adenosine(Non-covalent)

AYB.2: 24 residues within 4Å: Chain A: A.139, Y.143, L.146, R.167, E.169, E.174, H.175, L.176, F.179, M.181, N.183, E.233, L.234, S.235, S.236, V.238, W.254, G.256, A.257, G.258, F.259, G.260, R.263, I.274 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:Y.143, A:L.146, A:V.238, A:W.254 Hydrogen bonds: A:E.169, A:L.176, A:N.183, A:N.183, A:E.233, A:E.233, A:G.260 Water bridges: A:L.138, A:R.167, A:R.167, A:R.167 Salt bridges: A:R.167, A:R.167 pi-Stacking: A:F.179, A:F.179 pi-Cation interactions: A:R.263 AYB.4: 24 residues within 4Å: Chain B: A.139, Y.143, L.146, R.167, E.169, E.174, H.175, L.176, F.179, M.181, N.183, E.233, L.234, S.235, S.236, V.238, W.254, G.256, A.257, G.258, F.259, G.260, R.263, I.274 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:Y.143, B:L.146, B:V.238, B:W.254 Hydrogen bonds: B:E.169, B:L.176, B:N.183, B:N.183, B:E.233, B:E.233, B:G.260 Water bridges: B:L.138, B:R.167, B:R.167, B:R.167 Salt bridges: B:R.167, B:R.167 pi-Stacking: B:F.179, B:F.179 pi-Cation interactions: B:R.263

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yanagisawa, T. et al., Multistep Engineering of Pyrrolysyl-tRNA Synthetase to Genetically Encode N(varepsilon)-(o-Azidobenzyloxycarbonyl) lysine for Site-Specific Protein Modification. Chem.Biol. (2008)

Release Date

2008-12-02

Peptides

Pyrrolysyl-tRNA synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Pyrrolysyl-tRNA synthetase

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