SMTL ID : 2zin.1

Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase in complex with BocLys and an ATP analogue

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: R.167 Ligands: ANP.3 No protein-ligand interaction detected (PLIP) MG.2: 3 residues within 4Å: Chain A: E.233, S.236 Ligands: ANP.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.233, A:S.236, H2O.2 MG.6: 2 residues within 4Å: Chain B: R.167 Ligands: ANP.8 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain B: E.233, S.236 Ligands: ANP.8 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.233, B:S.236, H2O.11

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.3: 17 residues within 4Å: Chain A: R.167, E.169, H.175, L.176, F.179, M.181, E.233, L.234, S.235, S.236, G.258, F.259, G.260, R.263 Ligands: MG.1, MG.2, LBY.4 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:R.167, A:E.169, A:E.169, A:H.175, A:L.176, A:E.233, A:E.233, A:E.233, A:E.233, A:G.260, A:R.263, A:R.263 Water bridges: A:H.175, A:H.175, A:E.233 Salt bridges: A:R.167 pi-Stacking: A:F.179, A:F.179 pi-Cation interactions: A:R.263, A:R.263 ANP.8: 17 residues within 4Å: Chain B: R.167, E.169, H.175, L.176, F.179, M.181, E.233, L.234, S.235, S.236, G.258, F.259, G.260, R.263 Ligands: MG.6, MG.7, LBY.9 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:R.167, B:E.169, B:E.169, B:H.175, B:L.176, B:E.233, B:E.233, B:E.233, B:E.233, B:G.260, B:R.263, B:R.263 Water bridges: B:H.175, B:H.175, B:E.233 Salt bridges: B:R.167 pi-Stacking: B:F.179, B:F.179 pi-Cation interactions: B:R.263, B:R.263

2 x LBY: N~6~-(tert-butoxycarbonyl)-L-lysine(Non-covalent)

LBY.4: 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 Ligands: ANP.3, EDO.5 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.139, A:L.142, A:Y.143, A:W.254 Hydrogen bonds: A:N.183, A:G.256 Water bridges: A:A.139 LBY.9: 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 Ligands: ANP.8, EDO.10 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:A.139, B:L.142, B:Y.143, B:W.254 Hydrogen bonds: B:N.183, B:G.256 Water bridges: B:A.139

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

EDO.5: 6 residues within 4Å: Chain A: M.113, A.139, V.238, I.242, W.254 Ligands: LBY.4 No protein-ligand interaction detected (PLIP) EDO.10: 6 residues within 4Å: Chain B: M.113, A.139, V.238, I.242, W.254 Ligands: LBY.9 No protein-ligand interaction detected (PLIP)

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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