1BIO

HUMAN COMPLEMENT FACTOR D IN COMPLEX WITH ISATOIC ANHYDRIDE INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structures of native and complexed complement factor D: implications of the atypical His57 conformation and self-inhibitory loop in the regulation of specific serine protease activity.

Jing, H.Babu, Y.S.Moore, D.Kilpatrick, J.M.Liu, X.Y.Volanakis, J.E.Narayana, S.V.

(1998) J.Mol.Biol. 282: 1061-1081

  • DOI: 10.1006/jmbi.1998.2089
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Factor D is a serine protease essential for the activation of the alternative pathway of complement. The structures of native factor D and a complex formed with isatoic anhydride inhibitor were determined at resolution of 2.3 and 1.5 A, respectively, ...

    Factor D is a serine protease essential for the activation of the alternative pathway of complement. The structures of native factor D and a complex formed with isatoic anhydride inhibitor were determined at resolution of 2.3 and 1.5 A, respectively, in an isomorphous monoclinic crystal form containing one molecule per asymmetric unit. The native structure was compared with structures determined previously in a triclinic cell containing two molecules with different active site conformations. The current structure shows greater similarity with molecule B in the triclinic cell, suggesting that this may be the dominant factor D conformation in solution. The major conformational differences with molecule A in the triclinic cell are located in four regions, three of which are close to the active site and include some of the residues shown to be critical for factor D catalytic activity. The conformational flexibility associated with these regions is proposed to provide a structural basis for the previously proposed substrate-induced reversible conformational changes in factor D. The high-resolution structure of the factor D/isatoic anhydride complex reveals the binding mode of the mechanism-based inhibitor. The higher specificity towards factor D over trypsin and thrombin is based on hydrophobic interactions between the inhibitor benzyl ring and the aliphatic side-chain of Arg218 that is salt bridged with Asp189 at the bottom of the primary specificity (S1) pocket. Comparison of factor D structural variants with other serine protease structures revealed the presence of a unique "self-inhibitory loop". This loop (214-218) dictates the resting-state conformation of factor D by (1) preventing His57 from adopting active tautomer conformation, (2) preventing the P1 to P3 residues of the substrate from forming anti-parallel beta-sheets with the non-specific substrate binding loop, and (3) blocking the accessibility of Asp189 to the positive1y charged P1 residue of the substrate. The conformational switch from resting-state to active-state can only be induced by the single macromolecular substrate, C3b-bound factor B. This self-inhibitory mechanism is highly correlated with the unique functional properties of factor D, which include high specificity toward factor B, low esterolytic activity toward synthetic substrates, and absence of regulation by zymogen and serpin-like or other natural inhibitors in blood.


    Related Citations: 
    • Crystal Structure of a Complement Factor D Mutant Expressing Enhanced Catalytic Activity
      Kim, S.,Narayana, S.V.,Volanakis, J.E.
      (1995) J.Biol.Chem. 270: 24399
    • Erratum. Crystal Structure of a Complement Factor D Mutant Expressing Enhanced Catalytic Activity
      Kim, S.,Narayana, S.V.,Volanakis, J.E.
      (1995) J.Biol.Chem. 270: 31414
    • Structure of Human Factor D. A Complement System Protein at 2.0 A Resolution
      Narayana, S.V.,Carson, M.,El-Kabbani, O.,Kilpatrick, J.M.,Moore, D.,Chen, X.,Bugg, C.E.,Volanakis, J.E.,Delucas, L.J.
      (1994) J.Mol.Biol. 235: 695
    • Complement Factor D, a Novel Serine Protease
      Volanakis, J.E.,Narayana, S.V.
      (1996) Protein Sci. 5: 553
    • Crystallization and Preliminary X-Ray Investigation of Factor D of Human Complement
      Narayana, S.V.,Kilpatrick, J.M.,El-Kabbani, O.,Babu, Y.S.,Bugg, C.E.,Volanakis, J.E.,Delucas, L.J.
      (1991) J.Mol.Biol. 219: 1


    Organizational Affiliation

    Center for Macromolecular Crystallography, University of Alabama at Birmingham, Birmingham, AL 35294, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
COMPLEMENT FACTOR D
A
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
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
SOA
Query on SOA

Download SDF File 
Download CCD File 
A
ISATOIC ANHYDRIDE
C7 H9 N O
VYFOAVADNIHPTR-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SOAIC50: 2900 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.186 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 55.480α = 90.00
b = 49.910β = 105.69
c = 39.430γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
X-PLORrefinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-06-22
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance