SMTL ID : 4rqf.1

human Seryl-tRNA synthetase dimer complexed with one molecule of tRNAsec

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.50 Å

Oligo State

homo-dimer

Ligands

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

ANP.1: 10 residues within 4Å: Chain B: F.316, R.317, V.318, F.321, L.392, V.393, S.394, A.432, R.435 Ligands: SER.2 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:R.317, B:V.318, B:V.318, B:L.392, B:S.394, B:R.435, B:R.435 pi-Cation interactions: B:R.435 ANP.4: 11 residues within 4Å: Chain C: F.316, R.317, V.318, F.321, L.392, S.394, T.429, A.432, T.434, R.435 Ligands: SER.3 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:V.318, C:V.318, C:S.394, C:T.429, C:T.429, C:R.435, C:R.435 pi-Cation interactions: C:R.435

2 x SER: SERINE(Non-covalent)

SER.2: 7 residues within 4Å: Chain B: T.271, E.273, E.325, N.427, A.428, T.429 Ligands: ANP.1 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.271, B:E.273, B:E.325, B:N.427 SER.3: 9 residues within 4Å: Chain C: T.271, E.273, K.323, E.325, S.394, N.427, A.428, T.429 Ligands: ANP.4 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:T.271, C:E.273, C:K.323, C:N.427, C:A.428 Salt bridges: C:K.323

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, C. et al., SerRS-tRNASec complex structures reveal mechanism of the first step in selenocysteine biosynthesis. Nucleic Acids Res. (2015)

Release Date

2015-11-04

Peptides

Serine--tRNA ligase, cytoplasmic: BC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
A

C
B

Serine--tRNA ligase, cytoplasmic