SMTL ID : 2z67.1 (4 other biounits)

Crystal structure of archaeal O-phosphoseryl-tRNA(Sec) selenium transferase (SepSecS)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

4 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.1: 17 residues within 4Å: Chain A: S.158, T.159, G.160, H.186, S.188, P.189, T.240, F.241, N.267, A.269, Y.270, K.298 Chain B: E.91, R.92, P.325, G.326, R.327 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.241, A:K.298 Hydrogen bonds: A:T.159, A:G.160, A:S.188, A:S.188, A:N.267, A:K.298, B:R.327 pi-Stacking: A:H.186 Salt bridges: B:R.92 PLP.2: 15 residues within 4Å: Chain A: R.92, G.326, R.327 Chain B: S.158, T.159, G.160, H.186, S.188, P.189, T.240, F.241, N.267, A.269, Y.270, K.298 12 PLIP interactions: 8 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:F.241, B:A.269, B:K.298 Hydrogen bonds: B:T.159, B:G.160, B:S.188, B:N.267, A:R.327 pi-Stacking: B:H.186 Water bridges: A:R.92, A:R.92 Salt bridges: A:R.92 PLP.4: 15 residues within 4Å: Chain C: S.158, T.159, G.160, H.186, S.188, T.240, F.241, N.267, A.269, Y.270, S.295, K.298 Chain D: R.92, G.326, R.327 11 PLIP interactions: 9 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:F.241, C:A.269, C:K.298 Hydrogen bonds: C:T.159, C:G.160, C:S.188, C:S.188, C:N.267, D:R.327 pi-Stacking: C:H.186 Salt bridges: D:R.92 PLP.6: 15 residues within 4Å: Chain C: R.92, G.326, R.327 Chain D: S.158, T.159, G.160, H.186, S.188, P.189, T.240, F.241, N.267, A.269, Y.270, K.298 10 PLIP interactions: 8 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:F.241, D:A.269, D:K.298 Hydrogen bonds: D:T.159, D:G.160, D:S.188, D:N.267, C:R.327 pi-Stacking: D:H.186 Salt bridges: C:R.92

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 4 residues within 4Å: Chain B: R.114, S.115, Q.122, R.327 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.115, B:S.115, B:Q.122 Water bridges: B:S.115 Salt bridges: B:R.327 SO4.5: 4 residues within 4Å: Chain C: R.114, S.115, Q.122, R.327 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.115, C:Q.122 Salt bridges: C:R.114, C:R.327

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Araiso, Y. et al., Structural insights into RNA-dependent eukaryal and archaeal selenocysteine formation. Nucleic Acids Res. (2008)

Release Date

2008-04-29

Peptides

O-phosphoseryl-tRNA(Sec) selenium transferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

O-phosphoseryl-tRNA(Sec) selenium transferase

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