SMTL ID : 7rsm.1 (1 other biounit)

Crystal structure of pyrrolysyl-tRNA synthetase (N346D/C348S/Y384F) in complex with o-Chlorophenylalanine and AMP-PNP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

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

ANP.1: 13 residues within 4Å: Chain A: R.143, E.145, H.151, L.152, F.155, M.157, E.209, L.210, S.211, S.212, G.234, G.236, R.239 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:R.143, A:E.145, A:H.151, A:H.151, A:L.152, A:E.209, A:E.209, A:S.212, A:S.212, A:G.234, A:G.236, A:R.239, A:R.239 Water bridges: A:R.143 Salt bridges: A:R.143 pi-Stacking: A:F.155, A:F.155 ANP.3: 12 residues within 4Å: Chain B: R.143, E.145, H.151, L.152, F.155, E.209, L.210, S.211, S.212, G.234, G.236, R.239 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:R.143, B:E.145, B:E.145, B:H.151, B:H.151, B:H.151, B:L.152, B:E.209, B:E.209, B:E.209, B:E.209, B:S.212, B:S.212, B:G.236, B:R.239, B:R.239 Salt bridges: B:R.143 pi-Stacking: B:F.155, B:F.155

2 x 2L5: 2-chloro-L-phenylalanine(Non-covalent)

2L5.2: 11 residues within 4Å: Chain A: A.115, Y.119, L.122, D.159, F.160, S.161, S.212, W.230, G.232, A.233, G.234 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.115, A:L.122 pi-Stacking: A:Y.119 Halogen bonds: A:F.160 2L5.4: 12 residues within 4Å: Chain B: A.115, Y.119, L.122, D.159, F.160, S.161, S.212, V.214, W.230, G.232, A.233, G.234 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:A.115, B:L.122, B:W.230 Hydrogen bonds: B:D.159 Water bridges: B:D.159 pi-Stacking: B:Y.119 Halogen bonds: B:F.160

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vatansever, E.C. et al., A Designed, Highly Efficient Pyrrolysyl-tRNA Synthetase Mutant Binds o-Chlorophenylalanine Using Two Halogen Bonds. J.Mol.Biol. (2022)

Release Date

2022-07-20

Peptides

Pyrrolysine--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Pyrrolysine--tRNA ligase

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