SMTL ID : 2zce.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

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

2 x PYL: PYRROLYSINE(Non-covalent)

PYL.3: 16 residues within 4Å: Chain A: M.137, A.139, L.142, Y.143, R.167, M.181, N.183, F.184, C.185, S.236, V.238, W.254, G.256, A.257, G.258 Ligands: ANP.4 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.142, A:Y.143, A:V.238, A:W.254, A:W.254 Hydrogen bonds: A:N.183 Water bridges: A:L.138 Salt bridges: A:R.167 PYL.7: 16 residues within 4Å: Chain B: M.137, A.139, L.142, Y.143, R.167, M.181, N.183, F.184, C.185, S.236, V.238, W.254, G.256, A.257, G.258 Ligands: ANP.8 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.142, B:Y.143, B:V.238, B:W.254, B:W.254 Hydrogen bonds: B:N.183 Water bridges: B:L.138 Salt bridges: B:R.167

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

ANP.4: 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, PYL.3 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:R.167, A:E.169, A:H.175, A:L.176, A:E.233, A:E.233, A:E.233, A:G.260, A:R.263, A:R.263 Water bridges: A:H.175 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.5, MG.6, PYL.7 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:R.167, B:E.169, B:H.175, B:L.176, B:E.233, B:E.233, B:E.233, B:G.260, B:R.263, B:R.263 Water bridges: B:H.175 Salt bridges: B:R.167 pi-Stacking: B:F.179, B:F.179 pi-Cation interactions: B:R.263, B:R.263

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yanagisawa, T. et al., Crystallographic Studies on Multiple Conformational States of Active-site Loops in Pyrrolysyl-tRNA Synthetase. J.Mol.Biol. (2008)

Release Date

2008-04-22

Peptides

Pyrrolysyl-tRNA synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Pyrrolysyl-tRNA synthetase

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