› 3fd6

X-ray diffraction
1.95Å resolution

Crystal structure of human selenophosphate synthetase 1 complex with ADP and phosphate

Released:
DOI: 10.2210/pdb3fd6/pdb
PDB entry 3fd6 coloured by chain, front view.
PDB entry 3fd6 coloured by chain, side view.
PDB entry 3fd6 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystal structures of catalytic intermediates of human selenophosphate synthetase 1.
Wang KT, Wang J, Li LF, Su XD
J Mol Biol 390 747-59 (2009)
PMID: 19477186

Function and Biology Details

Reaction catalysed: 
ATP + selenide + H(2)O = AMP + selenophosphate + phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-156077 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Selenide, water dikinase 1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 394 amino acids
Theoretical weight: 43.1 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P49903 (Residues: 1-392; Coverage: 100%)
Gene names: SELD, SEPHS1, SPS, SPS1
Sequence domains:
Structure domains:

Ligands and Environments

4 bound ligands:
Ligand ADP 2 x ADP
Ligand PO4 2 x PO4
Ligand MG 6 x MG
Ligand NA 2 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BRUKER AXS MICROSTAR
Spacegroup: P43
Unit cell:
a: 67.618Å b: 67.618Å c: 182.551Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.133 0.13 0.196
Expression system: Escherichia coli

Quick links

Citations

1 review citation

The unique tRNASec and its role in selenocysteine biosynthesis.
Serrão et al. (2018)
9 other articles

1 mention without citation

Trypanosomatid selenophosphate synthetase structure, function and interaction with selenocysteine lyase.
da Silva et al. (2020)