PDBe 4ygc

X-ray diffraction
2.4Å resolution

Crystal structure of ERGIC-53/MCFD2, monoclinic calcium-bound form 1

Released:
Source organism: Homo sapiens
Entry authors: Satoh T, Nishio M, Yagi-Utsumi M, Suzuki K, Anzai T, Mizushima T, Kamiya Y, Kato K

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Protein ERGIC-53 Chains: A, C, E, G
Molecule details ›
Chains: A, C, E, G
Length: 246 amino acids
Theoretical weight: 27.15 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P49257 (Residues: 31-269; Coverage: 50%)
Gene names: ERGIC53, F5F8D, LMAN1
Sequence domains: Legume-like lectin family
Structure domains: Jelly Rolls
Multiple coagulation factor deficiency protein 2 Chains: B, D, F, H
Molecule details ›
Chains: B, D, F, H
Length: 104 amino acids
Theoretical weight: 12.06 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8NI22 (Residues: 67-146; Coverage: 67%)
Gene names: MCFD2, SDNSF
Sequence domains: EF-hand domain pair
Structure domains: EF-hand

Ligands and Environments

2 bound ligands:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL44XU
Spacegroup: P21
Unit cell:
a: 73.616Å b: 168.892Å c: 73.955Å
α: 90° β: 119.86° γ: 90°
R-values:
R R work R free
0.207 0.205 0.246
Expression system: Escherichia coli