› 7p74

X-ray diffraction
1.9Å resolution

The PDZ domain of SYNJ2BP complexed with the phosphorylated PDZ-binding motif of RSK1

Released:
DOI: 10.2210/pdb7p74/pdb
PDB entry 7p74 coloured by chain, front view.
PDB entry 7p74 coloured by chain, side view.
PDB entry 7p74 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Quantitative fragmentomics allow affinity mapping of interactomes.
Gogl G, Zambo B, Kostmann C, Cousido-Siah A, Morlet B, Durbesson F, Negroni L, Eberling P, Jané P, Nominé Y, Zeke A, Østergaard S, Monsellier É, Vincentelli R, Travé G
OpenAccess logo Nat Commun 13 5472 (2022)
PMID: 36115835

Function and Biology Details

Reaction catalysed: 
ATP + a protein = ADP + a phosphoprotein
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-139536 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Annexin A2; Synaptojanin-2-binding protein Chain: A
Molecule details ›
Chain: A
Length: 421 amino acids
Theoretical weight: 47.65 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P57105 (Residues: 6-103; Coverage: 68%)
  • Canonical: P07355 (Residues: 22-339; Coverage: 94%)
Gene names: ANX2, ANX2L4, ANXA2, CAL1H, LPC2D, OMP25, SYNJ2BP
Sequence domains:
Ribosomal protein S6 kinase alpha-1 Chain: B
Molecule details ›
Chain: B
Length: 15 amino acids
Theoretical weight: 1.83 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q15418 (Residues: 725-735; Coverage: 2%)
Gene names: MAPKAPK1A, RPS6KA1, RSK1

Ligands and Environments

2 bound ligands:
Ligand CA 4 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: SOLEIL BEAMLINE PROXIMA 2
Spacegroup: P212121
Unit cell:
a: 59.62Å b: 75.15Å c: 108.46Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.182 0.181 0.211
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 review citation

"It's Only a Model": When Protein Structure Predictions Need Experimental Validation, the Case of the HTLV-1 Tax Protein.
Guillon et al. (2024)
8 other articles

1 mention without citation

Quantitative fragmentomics allow affinity mapping of interactomes.
Gogl et al. (2022)