SMTL ID : 4rqe.1

human Seryl-tRNA synthetase dimer complexed with two molecules of tRNAsec

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 4.00 Å

Oligo State

homo-dimer

Ligands

2 x SER: SERINE(Non-covalent)

SER.1: 9 residues within 4Å: Chain A: T.271, E.273, R.302, E.325, S.394, N.427, A.428, T.429 Ligands: ANP.2 7 PLIP interactions: 6 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:E.273, A:S.394, A:S.394, A:N.427, A:T.429, S.1 Salt bridges: A:R.302 SER.3: 9 residues within 4Å: Chain B: T.271, E.273, R.302, E.325, K.376, S.394, N.427, T.429 Ligands: ANP.4 10 PLIP interactions: 1 Ligand-Ligand interactions, 9 interactions with chain B Hydrogen bonds: S.3, B:T.271, B:R.302, B:E.325, B:S.394, B:S.396, B:T.429, B:T.429, B:T.429 Salt bridges: B:K.376

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

ANP.2: 14 residues within 4Å: Chain A: R.302, E.304, F.316, R.317, V.318, F.321, E.391, L.392, V.393, S.394, T.429, A.432, R.435 Ligands: SER.1 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:R.302, A:R.317, A:R.317, A:R.317, A:V.318, A:V.318, A:L.392, A:V.393, A:S.394, A:T.429, A:R.435, A:R.435 Salt bridges: A:R.302 pi-Stacking: A:F.321 pi-Cation interactions: A:R.435, A:R.435 ANP.4: 16 residues within 4Å: Chain B: R.302, E.304, F.316, R.317, V.318, F.321, K.376, D.378, E.391, L.392, V.393, S.394, T.429, A.432, R.435 Ligands: SER.3 14 PLIP interactions: 2 Ligand-Ligand interactions, 12 interactions with chain B Hydrogen bonds: S.3, S.3, B:R.302, B:E.304, B:V.318, B:L.392, B:S.394, B:R.435, B:R.435 Salt bridges: B:R.302, B:K.376 pi-Stacking: B:F.321 pi-Cation interactions: B:R.435, B:R.435

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Serine--tRNA ligase, cytoplasmic