› 4d90

X-ray diffraction
2.6Å resolution

Crystal Structure of Del-1 EGF domains

Released:
DOI: 10.2210/pdb4d90/pdb
PDB entry 4d90 coloured by chain, front view.
PDB entry 4d90 coloured by chain, side view.
PDB entry 4d90 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
The RGD finger of Del-1 is a unique structural feature critical for integrin binding.
Schürpf T, Chen Q, Liu JH, Wang R, Springer TA, Wang JH
FASEB J 26 3412-20 (2012)
PMID: 22601780

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
monomeric (preferred)
homo dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-129152 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
EGF-like repeat and discoidin I-like domain-containing protein 3 Chains: A, B
Molecule details ›
Chains: A, B
Length: 143 amino acids
Theoretical weight: 15.24 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: O43854 (Residues: 24-157; Coverage: 29%)
Gene names: DEL1, EDIL3
Sequence domains:
Structure domains: Laminin

Ligands and Environments

4 bound ligands:
Ligand NGA 2 x NGA
Ligand NAG 2 x NAG
Ligand FUC 2 x FUC
Ligand CA 2 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C, APS BEAMLINE 19-ID
Spacegroup: P32
Unit cell:
a: 82.68Å b: 82.68Å c: 56.422Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.207 0.204 0.259
Expression system: Homo sapiens

Quick links

Citations

5 review citations

Breast cancer diagnosis: Imaging techniques and biochemical markers.
Jafari et al. (2018)
4 more

8 mentions without citation

Regulatory role of local tissue signal Del-1 in cancer and inflammation: a review.
Li et al. (2021)
7 more