› 5jsj

X-ray diffraction
2.35Å resolution

Crystal structure of Spindlin1 bound to compound EML631

Released:
DOI: 10.2210/pdb5jsj/pdb
PDB entry 5jsj coloured by chain, front view.
PDB entry 5jsj coloured by chain, side view.
PDB entry 5jsj coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Developing Spindlin1 small-molecule inhibitors by using protein microarrays.
Bae N, Viviano M, Su X, Lv J, Cheng D, Sagum C, Castellano S, Bai X, Johnson C, Khalil MI, Shen J, Chen K, Li H, Sbardella G, Bedford MT
Nat Chem Biol 13 750-756 (2017)
PMID: 28504676

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-195334 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Spindlin-1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 222 amino acids
Theoretical weight: 25.51 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9Y657 (Residues: 50-262; Coverage: 81%)
Gene names: OCR, SPIN, SPIN1
Sequence domains: Spin/Ssty Family
Structure domains: Spindlin/Ssty

Ligands and Environments

3 bound ligands:
Ligand 6PD 2 x 6PD
Ligand MG 1 x MG
Ligand CL 2 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL18U1
Spacegroup: P21
Unit cell:
a: 42.79Å b: 123.827Å c: 49.663Å
α: 90° β: 92.22° γ: 90°
R-values:
R R work R free
0.201 0.199 0.249
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 review citations

Targeting protein methylation: from chemical tools to precision medicines.
Dilworth et al. (2019)
1 more

3 mentions without citation

Chemical tools targeting readers of lysine methylation.
Ortiz et al. (2023)
2 more