SMTL ID : 3a4n.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 8 residues within 4Å: Chain A: L.12, P.13, G.14, V.15, G.16, K.17, S.18, R.120 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.14, A:V.15, A:G.16, A:K.17, A:S.18 Salt bridges: A:K.17, A:R.120 PO4.7: 8 residues within 4Å: Chain B: L.12, P.13, G.14, V.15, G.16, K.17, S.18, R.120 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:G.14, B:V.15, B:G.16, B:K.17, B:S.18 Water bridges: B:G.16, B:T.19 Salt bridges: B:K.17, B:R.120

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

IOD.2: 2 residues within 4Å: Chain A: K.131, R.223 Ligand excluded by PLIP IOD.8: 4 residues within 4Å: Chain B: V.128, K.131, R.199, R.223 Ligand excluded by PLIP

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

EDO.3: 5 residues within 4Å: Chain A: W.50, K.51, E.52, Y.205, K.246 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.52 Water bridges: A:K.53 EDO.4: 2 residues within 4Å: Chain A: K.60, R.64 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.60, A:R.64 EDO.5: 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.6: 1 residues within 4Å: Chain A: K.59 No protein-ligand interaction detected (PLIP) EDO.9: 1 residues within 4Å: Chain B: D.157 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.157, B:D.157 EDO.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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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