SMTL ID : 3add.1

Crystal structure of O-phosphoseryl-tRNA kinase complexed with selenocysteine tRNA and AMPPNP (crystal type 3)

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: 13 residues within 4Å: Chain A: L.19, P.20, G.21, V.22, G.23, K.24, S.25, T.26, D.48, R.123, R.127, T.161 Ligands: MG.2 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:G.21, A:V.22, A:G.23, A:K.24, A:K.24, A:S.25, A:T.26, A:T.26, A:D.48, A:R.123, A:R.127, A:R.127 Water bridges: A:K.24, A:S.25, A:S.25, A:S.25, A:S.25, A:T.87 Salt bridges: A:R.127 pi-Cation interactions: A:R.123, A:R.123 ANP.3: 14 residues within 4Å: Chain B: L.19, P.20, G.21, V.22, G.23, K.24, S.25, T.26, D.48, T.87, R.123, R.127, T.161 Ligands: MG.4 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:G.21, B:G.23, B:K.24, B:K.24, B:S.25, B:S.25, B:T.26, B:T.26, B:T.87, B:T.87, B:R.123, B:R.123, B:R.127, B:R.127 Water bridges: B:S.25, B:T.161, B:K.163 Salt bridges: B:R.127 pi-Cation interactions: B:R.123

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: S.25, D.85 Ligands: ANP.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.25, H2O.1, H2O.1, H2O.1 MG.4: 3 residues within 4Å: Chain B: S.25, D.85 Ligands: ANP.3 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:S.25, H2O.2, H2O.2, H2O.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chiba, S. et al., Structural Basis for the Major Role of O-Phosphoseryl-tRNA Kinase in the UGA-Specific Encoding of Selenocysteine. Mol.Cell (2010)

Release Date

2010-07-28

Peptides

L-seryl-tRNA(Sec) kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

L-seryl-tRNA(Sec) kinase

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