› 3fd5

X-ray diffraction
1.9Å resolution

Crystal structure of human selenophosphate synthetase 1 complex with AMPCP

Released:
DOI: 10.2210/pdb3fd5/pdb
PDB entry 3fd5 coloured by chain, front view.
PDB entry 3fd5 coloured by chain, side view.
PDB entry 3fd5 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 AP2 2 x AP2
Ligand PO4 2 x PO4
Ligand MG 6 x MG
Ligand K 2 x K
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007
Spacegroup: P43
Unit cell:
a: 66.734Å b: 66.734Å c: 181.168Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.14 0.138 0.195
Expression system: Escherichia coli

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Citations

1 review citation

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

5 mentions without citation

Widespread occurrence of covalent lysine-cysteine redox switches in proteins.
Rabe von Pappenheim et al. (2022)
4 more