› 7r2t

X-ray diffraction
2.5Å resolution

SYNJ2BP complex with a phosphorylated Vangl2 peptide at the P-1 position.

Released:
DOI: 10.2210/pdb7r2t/pdb
PDB entry 7r2t coloured by chain, front view.
PDB entry 7r2t coloured by chain, side view.
PDB entry 7r2t coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
PDZome-wide and structural characterization of the PDZ-binding motif of VANGL2.
Montserrat-Gomez M, Gogl G, Carrasco K, Betzi S, Durbesson F, Cousido-Siah A, Kostmann C, Essig DJ, Strømgaard K, Østergaard S, Morelli X, Trave G, Vincentelli R, Bailly E, Borg JP
Biochim Biophys Acta Proteins Proteom 1872 140989 (2024)
PMID: 38142947

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-232876 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Synaptojanin-2-binding protein Chain: A
Molecule details ›
Chain: A
Length: 422 amino acids
Theoretical weight: 47.77 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P57105 (Residues: 6-103, 105-108; Coverage: 70%)
Gene names: OMP25, SYNJ2BP
Sequence domains: PDZ domain
Vang-like protein 2 Chain: B
Molecule details ›
Chain: B
Length: 9 amino acids
Theoretical weight: 1.13 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q9ULK5 (Residues: 513-521; Coverage: 2%)
Gene names: KIAA1215, STB1, VANGL2

Ligands and Environments

2 bound ligands:
Ligand CA 5 x CA
Ligand GOL 2 x GOL
1 modified residue:
Ligand SEP 1 x SEP

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: P212121
Unit cell:
a: 60.1Å b: 61.38Å c: 145.31Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.218 0.217 0.239
Expression systems:
  • Escherichia coli
  • Not provided

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