› 4dw2

X-ray diffraction
2.97Å resolution

The crystal structure of uPA in complex with the Fab fragment of mAb-112

Released:
DOI: 10.2210/pdb4dw2/pdb
PDB entry 4dw2 coloured by chain, front view.
PDB entry 4dw2 coloured by chain, side view.
PDB entry 4dw2 coloured by chain, top view.
Source organisms:
Primary publication:
Rezymogenation of active urokinase induced by an inhibitory antibody.
Jiang L, Botkjaer KA, Andersen LM, Yuan C, Andreasen PA, Huang M
Biochem J 449 161-6 (2013)
PMID: 23016918

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 trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-208312 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Urokinase-type plasminogen activator chain B Chain: U
Molecule details ›
Chain: U
Length: 246 amino acids
Theoretical weight: 27.72 KDa
Source organism: Homo sapiens
Expression system: Komagataella pastoris
UniProt:
  • Canonical: P00749 (Residues: 179-424; Coverage: 60%)
Gene name: PLAU
Sequence domains: Trypsin
Structure domains: Trypsin-like serine proteases
Fab fragment of pro-uPA antibody mAb-112 Chain: H
Molecule details ›
Chain: H
Length: 212 amino acids
Theoretical weight: 22.89 KDa
Source organism: Mus musculus
Structure domains: Immunoglobulins
Fab fragment of pro-uPA antibody mAb-112 Chain: L
Molecule details ›
Chain: L
Length: 215 amino acids
Theoretical weight: 23.6 KDa
Source organism: Mus musculus
Structure domains: Immunoglobulins

Ligands and Environments

1 bound ligand:
Ligand SO4 1 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P212121
Unit cell:
a: 38.961Å b: 94.955Å c: 154.76Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.243 0.24 0.3
Expression system: Komagataella pastoris

Quick links

Citations

11 citation in other articles

Development of a 'mouse and human cross-reactive' affinity-matured exosite inhibitory human antibody specific to TACE (ADAM17) for cancer immunotherapy.
Kwok et al. (2014)
10 more

3 mentions without citation

Computationally-driven identification of antibody epitopes.
Hua et al. (2017)
2 more