› 2yd6

X-ray diffraction
1.35Å resolution

Crystal structure of the N-terminal Ig1-2 module of Human Receptor Protein Tyrosine Phosphatase Delta

Released:
DOI: 10.2210/pdb2yd6/pdb
PDB entry 2yd6 coloured by chain, front view.
PDB entry 2yd6 coloured by chain, side view.
PDB entry 2yd6 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Proteoglycan-specific molecular switch for RPTPσ clustering and neuronal extension.
Coles CH, Shen Y, Tenney AP, Siebold C, Sutton GC, Lu W, Gallagher JT, Jones EY, Flanagan JG, Aricescu AR
Science 332 484-8 (2011)
PMID: 21454754

Function and Biology Details

Reaction catalysed: 
Protein tyrosine phosphate + H(2)O = protein tyrosine + phosphate
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-149977 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Receptor-type tyrosine-protein phosphatase delta Chain: A
Molecule details ›
Chain: A
Length: 212 amino acids
Theoretical weight: 23.48 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P23468 (Residues: 21-226; Coverage: 11%)
Gene name: PTPRD
Sequence domains:
Structure domains: Immunoglobulins

Ligands and Environments

2 bound ligands:
Ligand CL 1 x CL
Ligand FLC 1 x FLC
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I02
Spacegroup: P3221
Unit cell:
a: 48.71Å b: 48.71Å c: 145.91Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.142 0.141 0.171
Expression system: Homo sapiens

Quick links

Citations

74 review citations

Demystifying heparan sulfate-protein interactions.
Xu et al. (2014)
73 more

5 mentions without citation

Structural basis of myelin-associated glycoprotein adhesion and signalling.
Pronker et al. (2016)
4 more