4D9R

Inhibiting Alternative Pathway Complement Activation by Targeting the Exosite on Factor D


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Inhibiting alternative pathway complement activation by targeting the factor d exosite.

Katschke, K.J.Wu, P.Ganesan, R.Kelley, R.F.Mathieu, M.A.Hass, P.E.Murray, J.Kirchhofer, D.Wiesmann, C.van Lookeren Campagne, M.

(2012) J.Biol.Chem. 287: 12886-12892

  • DOI: 10.1074/jbc.M112.345082
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • By virtue of its amplifying property, the alternative complement pathway has been implicated in a number of inflammatory diseases and constitutes an attractive therapeutic target. An anti-factor D Fab fragment (AFD) was generated to inhibit the alter ...

    By virtue of its amplifying property, the alternative complement pathway has been implicated in a number of inflammatory diseases and constitutes an attractive therapeutic target. An anti-factor D Fab fragment (AFD) was generated to inhibit the alternative complement pathway in advanced dry age-related macular degeneration. AFD potently prevented factor D (FD)-mediated proteolytic activation of its macromolecular substrate C3bB, but not proteolysis of a small synthetic substrate, indicating that AFD did not block access of the substrate to the catalytic site. The crystal structures of AFD in complex with human and cynomolgus FD (at 2.4 and 2.3 Å, respectively) revealed the molecular details of the inhibitory mechanism. The structures show that the AFD-binding site includes surface loops of FD that form part of the FD exosite. Thus, AFD inhibits FD proteolytic function by interfering with macromolecular substrate access rather than by inhibiting FD catalysis, providing the molecular basis of AFD-mediated inhibition of a rate-limiting step in the alternative complement pathway.


    Organizational Affiliation

    Department of Immunology, Genentech Incorporated, South San Francisco, California 94080, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Complement factor D
A, B
228Homo sapiensMutation(s): 0 
Gene Names: CFD (DF, PFD)
EC: 3.4.21.46
Find proteins for P00746 (Homo sapiens)
Go to Gene View: CFD
Go to UniProtKB:  P00746
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Fab light chain
L, D
214N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Fab heavy chain
H, E
218N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FABKd: 0.004 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.213 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 132.048α = 90.00
b = 132.048β = 90.00
c = 180.288γ = 90.00
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-02-22
    Type: Initial release
  • Version 1.1: 2012-03-14
    Type: Database references
  • Version 1.2: 2012-05-02
    Type: Database references
  • Version 1.3: 2013-09-18
    Type: Database references
  • Version 1.4: 2017-08-02
    Type: Advisory, Refinement description, Source and taxonomy