› 4wvp

X-ray diffraction
1.63Å resolution

Crystal structure of an activity-based probe HNE complex

Released:
DOI: 10.2210/pdb4wvp/pdb
PDB entry 4wvp coloured by chain, front view.
PDB entry 4wvp coloured by chain, side view.
PDB entry 4wvp coloured by chain, top view.
Source organisms:
Primary publication:
The elastase-PK101 structure: mechanism of an ultrasensitive activity-based probe revealed.
Lechtenberg BC, Kasperkiewicz P, Robinson H, Drag M, Riedl SJ
ACS Chem Biol 10 945-51 (2015)
PMID: 25581168

Function and Biology Details

Reaction catalysed: 
Hydrolysis of proteins, including elastin. Preferential cleavage Val-|- > Ala-|-.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
hetero dimer (preferred)
hetero hexamer
Assembly name:
PDBe Complex ID:
PDB-CPX-140066 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (4 distinct):
Neutrophil elastase Chain: E
Molecule details ›
Chain: E
Length: 218 amino acids
Theoretical weight: 23.32 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P08246 (Residues: 30-247; Coverage: 91%)
Gene names: ELA2, ELANE
Sequence domains: Trypsin
Structure domains: Trypsin-like serine proteases
BTN-3V3-NLB-OMT-OIC-3V2 Chain: I
Molecule details ›
Chain: I
Length: 6 amino acids
Theoretical weight: 1.15 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA, FUC
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, FUC
Carbohydrate polymer
2 bound ligands:
Ligand SO4 3 x SO4
Ligand EDO 6 x EDO
3 modified residues:
Ligand NLB 1 x NLB
Ligand OMT 1 x OMT
Ligand OIC 1 x OIC

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P63
Unit cell:
a: 73.12Å b: 73.12Å c: 69.451Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.14 0.138 0.169
Expression system: Not provided

Quick links

Citations

3 review citations

Emerging challenges in the design of selective substrates, inhibitors and activity-based probes for indistinguishable proteases.
Kasperkiewicz et al. (2017)
2 more

7 mentions without citation

Experimental and in silico evidence suggests vaccines are unlikely to be affected by D614G mutation in SARS-CoV-2 spike protein.
McAuley et al. (2020)
6 more