› 5hgg

X-ray diffraction
1.97Å resolution

Crystal structure of uPA in complex with a camelid-derived antibody fragment

Released:
DOI: 10.2210/pdb5hgg/pdb
PDB entry 5hgg coloured by chain, front view.
PDB entry 5hgg coloured by chain, side view.
PDB entry 5hgg coloured by chain, top view.
Source organisms:
Primary publication:
A Camelid-derived Antibody Fragment Targeting the Active Site of a Serine Protease Balances between Inhibitor and Substrate Behavior.
Kromann-Hansen T, Oldenburg E, Yung KW, Ghassabeh GH, Muyldermans S, Declerck PJ, Huang M, Andreasen PA, Ngo JC
J Biol Chem 291 15156-68 (2016)
PMID: 27226628

Function and Biology Details

Reaction catalysed: 
Specific cleavage of Arg-|-Val bond in plasminogen to form plasmin.
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-208313 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Urokinase-type plasminogen activator chain B Chains: A, B
Molecule details ›
Chains: A, B
Length: 246 amino acids
Theoretical weight: 27.72 KDa
Source organism: Homo sapiens
Expression system: Komagataella phaffii CBS 7435
UniProt:
  • Canonical: P00749 (Residues: 179-424; Coverage: 60%)
Gene name: PLAU
Sequence domains: Trypsin
Structure domains: Trypsin-like serine proteases
Camelid Derived Antibody Fragment, Nb4 Chains: S, T
Molecule details ›
Chains: S, T
Length: 128 amino acids
Theoretical weight: 13.6 KDa
Source organism: Vicugna pacos
Expression system: Escherichia coli
Structure domains: Immunoglobulins

Ligands and Environments

4 bound ligands:
Ligand GOL 5 x GOL
Ligand SO4 2 x SO4
Ligand TWN 3 x TWN
Ligand MES 1 x MES
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSRRC BEAMLINE BL13B1
Spacegroup: C2
Unit cell:
a: 186.985Å b: 77.749Å c: 61.454Å
α: 90° β: 102.4° γ: 90°
R-values:
R R work R free
0.169 0.167 0.196
Expression systems:
  • Komagataella phaffii CBS 7435
  • Escherichia coli

Quick links

Citations

7 review citations

Nanobody Technology: A Versatile Toolkit for Microscopic Imaging, Protein-Protein Interaction Analysis, and Protein Function Exploration.
Beghein et al. (2017)
6 more

4 mentions without citation

A Camelid-derived Antibody Fragment Targeting the Active Site of a Serine Protease Balances between Inhibitor and Substrate Behavior.
Kromann-Hansen et al. (2016)
3 more