4D9Q

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.189 

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:  4D9R

  • 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
Factor D
A, B
228Macaca mulattaGene Names: CFD
Find proteins for F6YBP7 (Macaca mulatta)
Go to Gene View: CFD
Go to UniProtKB:  F6YBP7
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Anti-Factor D, light chain
D, L
213N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Anti-Factor D, heavy chain
E, H
217N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, D, H, L
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, D, E, H
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.189 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 182.330α = 90.00
b = 80.760β = 107.19
c = 142.630γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
SCALAdata scaling
XSCALEdata scaling
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction

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: 2014-04-02
    Type: Structure summary
  • Version 1.4: 2017-08-02
    Type: Refinement description, Source and taxonomy