SMTL ID : 3a4l.1

Crystal structure of archaeal O-phosphoseryl-tRNA(Sec) kinase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

ANP.1: 14 residues within 4Å: Chain A: L.12, P.13, G.14, V.15, G.16, K.17, S.18, T.19, D.41, T.80, R.116, R.120, T.154 Ligands: MG.2 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:G.14, A:V.15, A:G.16, A:K.17, A:K.17, A:S.18, A:T.19, A:T.19, A:T.80, A:R.120, A:R.120, A:T.154 Water bridges: A:S.18, A:S.18, A:S.18, A:T.80, A:R.116 Salt bridges: A:R.120 pi-Cation interactions: A:R.116, A:R.116 ANP.6: 13 residues within 4Å: Chain B: L.12, P.13, G.14, V.15, G.16, K.17, S.18, T.19, T.80, R.116, R.120, T.154 Ligands: MG.7 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:G.14, B:V.15, B:G.16, B:K.17, B:K.17, B:K.17, B:S.18, B:T.19, B:T.19, B:D.41, B:R.120, B:R.120, B:T.154 Water bridges: B:S.18, B:S.18, B:S.18, B:T.80 Salt bridges: B:R.120 pi-Cation interactions: B:R.116, B:R.116

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: S.18 Ligands: ANP.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.18, H2O.9, H2O.15, H2O.33 MG.7: 2 residues within 4Å: Chain B: S.18 Ligands: ANP.6 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:S.18, H2O.170, H2O.186, H2O.295

2 x IOD: IODIDE ION(Non-functional Binders)

IOD.3: 1 residues within 4Å: Chain A: R.223 Ligand excluded by PLIP IOD.8: 2 residues within 4Å: Chain B: K.131, R.223 Ligand excluded by PLIP

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 4 residues within 4Å: Chain A: K.142, Y.143, K.144, W.145 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.142, A:K.144 EDO.5: 5 residues within 4Å: Chain A: E.45, S.46, F.47, P.48 Chain B: V.37 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.45 EDO.9: 3 residues within 4Å: Chain B: K.142, Y.143, K.144 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.144 EDO.10: 6 residues within 4Å: Chain A: K.22, V.37 Chain B: E.45, S.46, F.47, P.48 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.45

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Araiso, Y. et al., Structure of a tRNA-dependent kinase essential for selenocysteine decoding. Proc.Natl.Acad.Sci.USA (2009)

Release Date

2009-10-20

Peptides

L-seryl-tRNA(Sec) kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

L-seryl-tRNA(Sec) kinase

Related Entries With Identical Sequence