› 5e4k

X-ray diffraction
2.58Å resolution

Structure of ligand binding region of uPARAP at pH 7.4

Released:
DOI: 10.2210/pdb5e4k/pdb
PDB entry 5e4k coloured by chain, front view.
PDB entry 5e4k coloured by chain, side view.
PDB entry 5e4k coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystal structures of the ligand-binding region of uPARAP: effect of calcium ion binding.
Yuan C, Jürgensen HJ, Engelholm LH, Li R, Liu M, Jiang L, Luo Z, Behrendt N, Huang M
Biochem J 473 2359-68 (2016)
PMID: 27247422

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-193652 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
C-type mannose receptor 2 Chain: A
Molecule details ›
Chain: A
Length: 492 amino acids
Theoretical weight: 55.88 KDa
Source organism: Homo sapiens
Expression system: Drosophila melanogaster
UniProt:
  • Canonical: Q9UBG0 (Residues: 31-510; Coverage: 33%)
Gene names: CLEC13E, ENDO180, KIAA0709, MRC2, UPARAP
Sequence domains:

Ligands and Environments

5 bound ligands:
Ligand CA 2 x CA
Ligand NA 1 x NA
Ligand NAG 2 x NAG
Ligand 1PE 1 x 1PE
Ligand PE5 1 x PE5
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P41212
Unit cell:
a: 74.94Å b: 74.94Å c: 224.57Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.216 0.214 0.257
Expression system: Drosophila melanogaster

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Citations

1 review citation

uPARAP/Endo180: a multifaceted protein of mesenchymal cells.
Gucciardo et al. (2022)
2 other articles