› 4dy7

X-ray diffraction
2.8Å resolution

Crystal structures of protease nexin-1 in complex with S195A thrombin

Released:
DOI: 10.2210/pdb4dy7/pdb
PDB entry 4dy7 coloured by chain, front view.
PDB entry 4dy7 coloured by chain, side view.
PDB entry 4dy7 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

Reaction catalysed: 
Selective cleavage of Arg-|-Gly bonds in fibrinogen to form fibrin and release fibrinopeptides A and B.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-133071 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Thrombin light chain Chains: A, D
Molecule details ›
Chains: A, D
Length: 49 amino acids
Theoretical weight: 5.64 KDa
Source organism: Homo sapiens
Expression system: Cricetinae gen. sp.
UniProt:
  • Canonical: P00734 (Residues: 315-363; Coverage: 8%)
Gene name: F2
Sequence domains: Thrombin light chain
Structure domains: Thrombin light chain domain
Thrombin heavy chain Chains: B, E
Molecule details ›
Chains: B, E
Length: 259 amino acids
Theoretical weight: 29.76 KDa
Source organism: Homo sapiens
Expression system: Cricetinae gen. sp.
UniProt:
  • Canonical: P00734 (Residues: 364-622; Coverage: 43%)
Gene name: F2
Sequence domains: Trypsin
Structure domains: Trypsin-like serine proteases
Glia-derived nexin Chains: C, F
Molecule details ›
Chains: C, F
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

3 bound ligands:
Ligand ACT 3 x ACT
Ligand CA 2 x CA
Ligand NA 1 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I02
Spacegroup: C2
Unit cell:
a: 191.96Å b: 86.67Å c: 101.89Å
α: 90° β: 94.44° γ: 90°
R-values:
R R work R free
0.225 0.223 0.268
Expression systems:
  • Cricetinae gen. sp.
  • Escherichia coli

Quick links

Citations

4 review citations

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

2 mentions without citation

1.45 Å resolution structure of SRPN18 from the malaria vector Anopheles gambiae.
Meekins et al. (2016)
1 more