› 6dn8

X-ray diffraction
1.75Å resolution

SPRY domain-containing SOCS box protein 2 complexed with (GZJ)VDINNN(CY3) Cyclic peptide inhibitor

Released:
DOI: 10.2210/pdb6dn8/pdb
PDB entry 6dn8 coloured by chain, front view.
PDB entry 6dn8 coloured by chain, side view.
PDB entry 6dn8 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
A Cyclic Peptide Inhibitor of the iNOS-SPSB Protein-Protein Interaction as a Potential Anti-Infective Agent.
Sadek MM, Barlow N, Leung EWW, Williams-Noonan BJ, Yap BK, Shariff FM, Caradoc-Davies TT, Nicholson SE, Chalmers DK, Thompson PE, Law RHP, Norton RS
ACS Chem Biol 13 2930-2938 (2018)
PMID: 30226743

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-166612 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
SPRY domain-containing SOCS box protein 4 Chains: A, C, E
Molecule details ›
Chains: A, C, E
Length: 229 amino acids
Theoretical weight: 25.23 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: Q96A44 (Residues: 28-233; Coverage: 76%)
Gene names: SPSB4, SSB4
Sequence domains: SPRY domain
(GZJ)VDINNN(CY3) Cyclic peptide inhibitor Chains: B, D, F
Molecule details ›
Chains: B, D, F
Length: 8 amino acids
Theoretical weight: 917 Da
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand ACT 3 x ACT
Ligand SO4 3 x SO4
1 modified residue:
Ligand CY3 3 x CY3

Experiments and Validation Details

Entry percentile scores
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX2
Unit cell:
a: 49.02Å b: 109.37Å c: 118.1Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.194 0.193 0.21
Expression systems:
  • Escherichia coli K-12
  • Not provided

Quick links

Citations

2 review citations

E3 Ligase Ligands for PROTACs: How They Were Found and How to Discover New Ones.
Ishida et al. (2021)
1 more