SMTL ID : 3vqy.1

Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase in complex with BocLys and AMPPNP (form 2)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

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

ANP.1: 16 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, G.260, R.263 Ligands: LBY.2, MG.3, MG.4 17 PLIP interactions: 17 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 Salt bridges: A:R.167 pi-Stacking: A:F.179, A:F.179 pi-Cation interactions: A:R.263, A:R.263 ANP.5: 16 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, G.260, R.263 Ligands: LBY.6, MG.7, MG.8 17 PLIP interactions: 17 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 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.2: 11 residues within 4Å: Chain A: M.113, A.139, Y.143, N.183, S.236, V.238, I.242, W.254, A.257, G.258 Ligands: ANP.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.139, A:V.238, A:I.242, A:W.254 Hydrogen bonds: A:N.183, A:S.236 LBY.6: 11 residues within 4Å: Chain B: M.113, A.139, Y.143, N.183, S.236, V.238, I.242, W.254, A.257, G.258 Ligands: ANP.5 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:A.139, B:V.238, B:I.242, B:W.254 Hydrogen bonds: B:N.183, B:S.236

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: E.120, R.167 Ligands: ANP.1 No protein-ligand interaction detected (PLIP) MG.4: 3 residues within 4Å: Chain A: E.233, S.236 Ligands: ANP.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.233, A:E.233, A:S.236, H2O.2 MG.7: 3 residues within 4Å: Chain B: E.120, R.167 Ligands: ANP.5 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain B: E.233, S.236 Ligands: ANP.5 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.233, B:E.233, B:S.236, H2O.6

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yanagisawa, T. et al., A novel crystal form of pyrrolysyl-tRNA synthetase reveals the pre- and post-aminoacyl-tRNA synthesis conformational states of the adenylate and aminoacyl moieties and an asparagine residue in the catalytic site. Acta Crystallogr.,Sect.D (2013)

Release Date

2013-01-02

Peptides

Pyrrolysine--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Pyrrolysine--tRNA ligase

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