› 8aak

X-ray diffraction
2.55Å resolution

Crystal structure of the PDZ tandem of syntenin in complex with compound 29

Released:
DOI: 10.2210/pdb8aak/pdb
PDB entry 8aak coloured by chain, front view.
PDB entry 8aak coloured by chain, side view.
PDB entry 8aak coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Discovery of a PDZ Domain Inhibitor Targeting the Syndecan/Syntenin Protein-Protein Interaction: A Semi-Automated "Hit Identification-to-Optimization" Approach.
Hoffer L, Garcia M, Leblanc R, Feracci M, Betzi S, Ben Yaala K, Daulat AM, Zimmermann P, Roche P, Barral K, Morelli X
J Med Chem 66 4633-4658 (2023)
PMID: 36939673

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-126347 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Syntenin-1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 166 amino acids
Theoretical weight: 18.02 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O00560 (Residues: 113-273; Coverage: 54%)
Gene names: MDA9, SDCBP, SYCL
Sequence domains: PDZ domain

Ligands and Environments

2 bound ligands:
Ligand LL6 2 x LL6
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SOLEIL BEAMLINE PROXIMA 1
Spacegroup: P212121
Unit cell:
a: 34.66Å b: 96.91Å c: 103.82Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.218 0.214 0.282
Expression system: Escherichia coli

Quick links