SMTL ID : 3a4m.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

homo-dimer

Ligands

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 11 residues within 4Å: Chain A: L.12, G.14, V.15, G.16, K.17, S.18, T.19, R.116, R.120, T.154 Ligands: MG.2 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:G.14, A:V.15, A:G.16, A:K.17, A:S.18, A:T.19, A:T.19 Water bridges: A:R.120, A:R.120, A:R.120, A:R.120, A:T.154 Salt bridges: A:K.17, A:R.120, A:R.120 pi-Cation interactions: A:R.116, A:R.116 ADP.5: 12 residues within 4Å: Chain B: L.12, P.13, G.14, V.15, G.16, K.17, S.18, T.19, R.116, R.120, T.154 Ligands: MG.6 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:G.14, B:V.15, B:G.16, B:K.17, B:S.18, B:T.19, B:T.19, B:R.120, B:T.154 Water bridges: B:S.18 Salt bridges: B:K.17, 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: ADP.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.18, H2O.1, H2O.1, H2O.1, H2O.1 MG.6: 2 residues within 4Å: Chain B: S.18 Ligands: ADP.5 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:S.18, H2O.6, H2O.6, H2O.6, H2O.7

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

IOD.3: 2 residues within 4Å: Chain A: R.199, R.223 Ligand excluded by PLIP IOD.7: 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: 7 residues within 4Å: Chain A: E.45, S.46, F.47, P.48 Chain B: K.22, A.25, V.37 No protein-ligand interaction detected (PLIP) EDO.8: 5 residues within 4Å: Chain A: K.22, V.37 Chain B: E.45, S.46, P.48 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.45 EDO.9: 3 residues within 4Å: Chain B: Y.143, K.144, W.145 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.144 EDO.10: 6 residues within 4Å: Chain B: E.55, E.56, K.59, K.193, K.196, E.197 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.56, B:E.56, B:K.193, B:K.196, B:E.197 Water bridges: B:E.55

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

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