› 5pyt

X-ray diffraction
2.13Å resolution

PanDDA analysis group deposition -- Crystal Structure of SP100 after initial refinement with no ligand modelled (structure 89)

Released:
DOI: 10.2210/pdb5pyt/pdb
PDB entry 5pyt coloured by chain, front view.
PDB entry 5pyt coloured by chain, side view.
PDB entry 5pyt coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density.
Pearce NM, Krojer T, Bradley AR, Collins P, Nowak RP, Talon R, Marsden BD, Kelm S, Shi J, Deane CM, von Delft F
OpenAccess logo Nat Commun 8 15123 (2017)
PMID: 28436492

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-149985 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Nuclear autoantigen Sp-100 Chains: A, B
Molecule details ›
Chains: A, B
Length: 180 amino acids
Theoretical weight: 21.5 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P23497 (Residues: 466-498, 499-508; Coverage: 5%)
  • Best match: P23497-4 (Residues: 700-879)
Gene name: SP100
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand ZN 5 x ZN
Ligand MES 1 x MES
Ligand EDO 2 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: C2
Unit cell:
a: 127.59Å b: 45.41Å c: 83.5Å
α: 90° β: 101.94° γ: 90°
R-values:
R R work R free
0.395 0.394 0.418
Expression system: Escherichia coli

Quick links

Citations

16 review citations

WD40 repeat domain proteins: a novel target class?
Schapira et al. (2017)
15 more