› 5wy8

X-ray diffraction
3.07Å resolution

Crystal structure of PTP delta Ig1-Ig3 in complex with IL1RAPL1 Ig1-Ig3

Released:
DOI: 10.2210/pdb5wy8/pdb
PDB entry 5wy8 coloured by chain, front view.
PDB entry 5wy8 coloured by chain, side view.
PDB entry 5wy8 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
LAR-RPTP Clustering Is Modulated by Competitive Binding between Synaptic Adhesion Partners and Heparan Sulfate.
Won SY, Kim CY, Kim D, Ko J, Um JW, Lee SB, Buck M, Kim E, Heo WD, Lee JO, Kim HM
Front Mol Neurosci 10 327 (2017)
PMID: 29081732

Function and Biology Details

Reactions catalysed: 
Protein tyrosine phosphate + H(2)O = protein tyrosine + phosphate
(1a) NAD(+) = cyclic ADP-ribose + nicotinamide
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-149976 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (5 distinct):
Receptor-type tyrosine-protein phosphatase delta Chain: A
Molecule details ›
Chain: A
Length: 298 amino acids
Theoretical weight: 32.73 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P23468 (Residues: 21-318; Coverage: 16%)
Gene name: PTPRD
Sequence domains:
Interleukin-1 receptor accessory protein-like 1 Chain: B
Molecule details ›
Chain: B
Length: 323 amino acids
Theoretical weight: 37.01 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q9NZN1 (Residues: 27-349; Coverage: 48%)
Gene names: IL1RAPL1, OPHN4
Sequence domains:
Structure domains: Immunoglobulins

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, FUC
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
2 bound ligands:
Ligand NAG 2 x NAG
Ligand ZN 3 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PAL/PLS BEAMLINE 7A (6B, 6C1)
Spacegroup: P3212
Unit cell:
a: 110.416Å b: 110.416Å c: 210.536Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.234 0.232 0.255
Expression system: Spodoptera frugiperda

Quick links

Citations

2 review citations

SALM/Lrfn Family Synaptic Adhesion Molecules.
Lie et al. (2018)
1 more

3 mentions without citation

Structural Basis of IL-1 Family Cytokine Signaling.
Fields et al. (2019)
2 more