› 8aai

X-ray diffraction
2.76Å resolution

Crystal structure of the PDZ tandem of syntenin in complex with fragment E5

Released:
DOI: 10.2210/pdb8aai/pdb
PDB entry 8aai coloured by chain, front view.
PDB entry 8aai coloured by chain, side view.
PDB entry 8aai 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, C, D
Molecule details ›
Chains: A, B, C, D
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

1 bound ligand:
Ligand LKV 4 x LKV
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: P1
Unit cell:
a: 29.114Å b: 56.13Å c: 102.867Å
α: 82.71° β: 83.462° γ: 77.033°
R-values:
R R work R free
0.277 0.275 0.317
Expression system: Escherichia coli

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