Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - ABC Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer -A2B 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 75206.37 
• Atom Count: 5067 
• Residue Count: 679 
• Unique protein chains: 3

4OGX

Crystal structure of Fab DX-2930 in complex with human plasma kallikrein at 2.4 Angstrom resolution

• DOI: 10.2210/pdb4OGX/pdb

• Classification: HYDROLASE/ANTIBODY
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda, Escherichia coli
• Mutation(s): 4 


• Deposited: 2014-01-16 Released: 2014-07-09 
• Deposition Author(s): Edwards, T.E., Clifton, M.C., Abendroth, J., Nixon, A., Ladner, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.236 
• R-Value Work: 0.185 

Literature

Inhibition of plasma kallikrein by a highly specific active site blocking antibody.

Kenniston, J.A., Faucette, R.R., Martik, D., Comeau, S.R., Lindberg, A.P., Kopacz, K.J., Conley, G.P., Chen, J., Viswanathan, M., Kastrapeli, N., Cosic, J., Mason, S., DiLeo, M., Abendroth, J., Kuzmic, P., Ladner, R.C., Edwards, T.E., TenHoor, C., Adelman, B.A., Nixon, A.E., Sexton, D.J.

(2014) J.Biol.Chem. 289: 23596-23608

• PubMed: 24970892 
• DOI: 10.1074/jbc.M114.569061
• Primary Citation of Related Structures:  
  4PUB, 4OGY


• PubMed Abstract: 
  

Plasma kallikrein (pKal) proteolytically cleaves high molecular weight kininogen to generate the potent vasodilator and the pro-inflammatory peptide, bradykinin. pKal activity is tightly regulated in healthy individuals by the serpin C1-inhibitor, but individuals with hereditary angioedema (HAE) are deficient in C1-inhibitor and consequently exhibit excessive bradykinin generation that in turn causes debilitating and potentially fatal swelling attacks. To develop a potential therapeutic agent for HAE and other pKal-mediated disorders, we used phage display to discover a fully human IgG1 monoclonal antibody (DX-2930) against pKal. In vitro experiments demonstrated that DX-2930 potently inhibits active pKal (Ki = 0.120 ± 0.005 nM) but does not target either the zymogen (prekallikrein) or any other serine protease tested. These findings are supported by a 2.1-Å resolution crystal structure of pKal complexed to a DX-2930 Fab construct, which establishes that the pKal active site is fully occluded by the antibody. DX-2930 injected subcutaneously into cynomolgus monkeys exhibited a long half-life (t½ ∼ 12.5 days) and blocked high molecular weight kininogen proteolysis in activated plasma in a dose- and time-dependent manner. Furthermore, subcutaneous DX-2930 reduced carrageenan-induced paw edema in rats. A potent and long acting inhibitor of pKal activity could be an effective treatment option for pKal-mediated diseases, such as HAE.

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Organizational Affiliation: 

From the Dyax Corp., Burlington, Massachusetts 01803.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Plasma kallikrein	A	241	Homo sapiens	Mutation(s): 4  Gene Names: KLKB1 (KLK3) EC: 3.4.21.34
Find proteins for P03952 (Homo sapiens) Go to Gene View: KLKB1 Go to UniProtKB:  P03952

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
DX-2930 HEAVY CHAIN	H	225	Homo sapiens	Mutation(s): 0
Find proteins for S6C4R2 (Homo sapiens) Go to UniProtKB:  S6C4R2

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
DX-2930 LIGHT CHAIN	L	213	Homo sapiens	Mutation(s): 0
Find proteins for Q7Z3Y4 (Homo sapiens) Go to UniProtKB:  Q7Z3Y4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.236 
• R-Value Work: 0.185 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 109.610	α = 90.00
b = 171.500	β = 90.00
c = 42.320	γ = 90.00

Software Package:

Software Name	Purpose
XDS	data reduction
StructureStudio	data collection
PHASER	phasing
PDB_EXTRACT	data extraction
XSCALE	data scaling
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-01-16 
• Released Date: 2014-07-09 
• Deposition Author(s): Edwards, T.E., Clifton, M.C., Abendroth, J., Nixon, A., Ladner, R.

Revision History 

• Version 1.0: 2014-07-09
  Type: Initial release
• Version 1.1: 2014-09-10
  Type: Database references