› 7d7p

X-ray diffraction
2.1Å resolution

Crystal structure of the phosphodiesterase domain of Salpingoeca rosetta rhodopsin phosphodiesterase

Released:
DOI: 10.2210/pdb7d7p/pdb
PDB entry 7d7p coloured by chain, front view.
PDB entry 7d7p coloured by chain, side view.
PDB entry 7d7p coloured by chain, top view.
Source organism: Salpingoeca rosetta
Primary publication:
Structural insights into the mechanism of rhodopsin phosphodiesterase.
Ikuta T, Shihoya W, Sugiura M, Yoshida K, Watari M, Tokano T, Yamashita K, Katayama K, Tsunoda SP, Uchihashi T, Kandori H, Nureki O
OpenAccess logo Nat Commun 11 5605 (2020)
PMID: 33154353

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-123407 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Phosphodiesterase Chain: A
Molecule details ›
Chain: A
Length: 365 amino acids
Theoretical weight: 42.02 KDa
Source organism: Salpingoeca rosetta
Expression system: Homo sapiens
UniProt:
  • Canonical: F2TZN0 (Residues: 346-703; Coverage: 51%)
Gene name: PTSG_02023
Sequence domains: 3'5'-cyclic nucleotide phosphodiesterase

Ligands and Environments

5 bound ligands:
Ligand 2PE 1 x 2PE
Ligand PEG 1 x PEG
Ligand EDO 3 x EDO
Ligand ZN 1 x ZN
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL32XU
Spacegroup: C2
Unit cell:
a: 117.2Å b: 67.54Å c: 56.89Å
α: 90° β: 110.82° γ: 90°
R-values:
R R work R free
0.191 0.188 0.24
Expression system: Homo sapiens

Quick links

Citations

5 review citations

Towards the Idea of Molecular Brains.
Timsit et al. (2021)
4 more