4OGY | pdb_00004ogy

Crystal structure of Fab DX-2930 in complex with human plasma kallikrein at 2.1 Angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.221 (Depositor), 0.228 (DCC) 
  • R-Value Work: 
    0.183 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.185 (Depositor) 

Starting Models: experimental
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This is version 1.3 of the entry. See complete history

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 Biological Chem 289: 23596-23608

  • DOI: https://doi.org/10.1074/jbc.M114.569061
  • Primary Citation Related Structures: 
    4OGX, 4OGY, 4PUB

  • 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.


  • Organizational Affiliation
    • From the Dyax Corp., Burlington, Massachusetts 01803.

Macromolecule Content 

  • Total Structure Weight: 149.45 kDa 
  • Atom Count: 11,073 
  • Modeled Residue Count: 1,321 
  • Deposited Residue Count: 1,358 
  • Unique protein chains: 3

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Plasma kallikrein
A, B
241Homo sapiensMutation(s): 4 
Gene Names: KLK3KLKB1KLKB1_HUMAN
EC: 3.4.21.34
UniProt & NIH Common Fund Data Resources
Find proteins for P03952 (Homo sapiens)
Explore P03952 
Go to UniProtKB:  P03952
PHAROS:  P03952
GTEx:  ENSG00000164344 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03952
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
DX-2930 HEAVY CHAINC [auth H],
E [auth M]
225Homo sapiensMutation(s): 0 
UniProt
Find proteins for S6C4R2 (Homo sapiens)
Explore S6C4R2 
Go to UniProtKB:  S6C4R2
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UniProt GroupS6C4R2
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
DX-2930 LIGHT CHAIND [auth L],
F [auth N]
213Homo sapiensMutation(s): 0 
UniProt
Find proteins for Q7Z3Y4 (Homo sapiens)
Explore Q7Z3Y4 
Go to UniProtKB:  Q7Z3Y4
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UniProt GroupQ7Z3Y4
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.221 (Depositor), 0.228 (DCC) 
  • R-Value Work:  0.183 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.185 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.12α = 90
b = 113.76β = 94.7
c = 89.05γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-09-10
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-11-27
    Changes: Structure summary