› 1w9o

X-ray diffraction
2.25Å resolution

Crystal structure of the PDZ tandem of human syntenin in complex with TNEYYV peptide

Released:
DOI: 10.2210/pdb1w9o/pdb
PDB entry 1w9o coloured by chain, front view.
PDB entry 1w9o coloured by chain, side view.
PDB entry 1w9o coloured by chain, top view.
Source organisms:
Primary publication:
The binding of the PDZ tandem of syntenin to target proteins.
Grembecka J, Cierpicki T, Devedjiev Y, Derewenda U, Kang BS, Bushweller JH, Derewenda ZS
Biochemistry 45 3674-83 (2006)
PMID: 16533050

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-126345 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
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 BL21
UniProt:
  • Canonical: O00560 (Residues: 113-273; Coverage: 54%)
Gene names: MDA9, SDCBP, SYCL
Sequence domains: PDZ domain
Structure domains: Pdz3 Domain
TNEYYV PEPTIDE Chains: S, T
Molecule details ›
Chains: S, T
Length: 6 amino acids
Theoretical weight: 788 Da
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand BEZ 1 x BEZ
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X9B
Spacegroup: P41212
Unit cell:
a: 72.134Å b: 72.134Å c: 126.221Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.218 0.214 0.281
Expression systems:
  • Escherichia coli BL21
  • Not provided

Quick links

Citations

15 review citations

Organization and dynamics of PDZ-domain-related supramodules in the postsynaptic density.
Feng et al. (2009)
14 more

3 mentions without citation

A PDZ Protein MDA-9/Syntenin: As a Target for Cancer Therapy.
Yu et al. (2019)
2 more