› 4dy0

X-ray diffraction
2.35Å resolution

Crystal structure of native protease nexin-1 with heparin

Released:
DOI: 10.2210/pdb4dy0/pdb
PDB entry 4dy0 coloured by chain, front view.
PDB entry 4dy0 coloured by chain, side view.
PDB entry 4dy0 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystal structures of protease nexin-1 in complex with heparin and thrombin suggest a 2-step recognition mechanism.
Li W, Huntington JA
Blood 120 459-67 (2012)
PMID: 22618708

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
monomeric (preferred)
homo dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-139364 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Glia-derived nexin Chains: A, B
Molecule details ›
Chains: A, B
Length: 379 amino acids
Theoretical weight: 41.92 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P07093 (Residues: 20-398; Coverage: 100%)
Gene names: PI7, PN1, SERPINE2
Sequence domains: Serpin (serine protease inhibitor)
Structure domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: IDS, SGN
Carbohydrate polymer
2 bound ligands:
Ligand SO4 4 x SO4
Ligand GOL 2 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P41212
Unit cell:
a: 140.65Å b: 140.65Å c: 93.55Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.184 0.182 0.226
Expression system: Escherichia coli

Quick links

Citations

4 review citations

Thrombin inhibition by the serpins.
Huntington JA. (2013)
3 more

4 mentions without citation

A Comprehensive Phylogenetic Analysis of the Serpin Superfamily.
Spence et al. (2021)
3 more