Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 49.21 kDa 
• Atom Count: 3706 
• Residue Count: 456 
• Unique protein chains: 1

1DFP

FACTOR D INHIBITED BY DIISOPROPYL FLUOROPHOSPHATE

• DOI: 10.2210/pdb1DFP/pdb

• Classification: SERINE PROTEASE
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 1997-02-18 Released: 1998-02-25 
• Deposition Author(s): Cole, L.B., Chu, N., Kilpatrick, J.M., Volanakis, J.E., Narayana, S.V.L., Babu, Y.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.228 
• R-Value Work: 0.148 
• R-Value Observed: 0.148 

Literature

Structure of diisopropyl fluorophosphate-inhibited factor D.

Cole, L.B., Chu, N., Kilpatrick, J.M., Volanakis, J.E., Narayana, S.V., Babu, Y.S.

(1997) Acta Crystallogr D Biol Crystallogr 53: 143-150

• PubMed: 15299948 
• DOI: 10.1107/S0907444996012991
• Primary Citation of Related Structures:  
  1DFP


• PubMed Abstract: 
  

Factor D (D) is a serine protease, crucial for the activation of the alternative complement pathway. Only a limited number of general serine protease inhibitors are known to inhibit D, most of which covalently bind to the serine hydroxyl of the catalytic triad. The structure of the first enzyme:inhibitor covalent adduct of D with diisopropyl fluorophosphate (DIP:D) to a resolution of 2.4 A is described. The inhibited enzyme is similar in overall structure to the native enzyme and to trypsin, yet exhibits notable differences in the active site. One region of the active site is conserved between D and trypsin with respect to amino-acid sequence and to conformation. Another reflects the amino-acid substitutions and conformational flexibility between these enzymes. The active-site histidine residue is observed in the gauche+ conformation, not the normal gauche- orientation seen in the classic catalytic triad arrangement required for enzymatic activity in serine proteases. Comparisons of the active sites between native D, the DIP:D adduct, and DIP-inhibited trypsin have provided fundamental insights currently being employed in the design of novel small-molecule pharmaceutical agents capable of modulating the alternative complement pathway.

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Organizational Affiliation: 

BioCryst Pharmaceuticals, Inc., Birmingham, AL 35244-2812, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FACTOR D	A, B	228	Homo sapiens	Mutation(s): 0  Gene Names: CFD, DF, PFD EC: 3.4.21.46
Find proteins for P00746 (Homo sapiens) Explore P00746  Go to UniProtKB:  P00746
NIH Common Fund Data Resources
PHAROS:  P00746 GTEx:  ENSG00000197766

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DFP	A, B	DIISOPROPYL PHOSPHONATE C6 H15 O3 P BLKXLEPPVDUHBY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.228 
• R-Value Work: 0.148 
• R-Value Observed: 0.148 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.6	α = 90
b = 125.7	β = 110.05
c = 41.9	γ = 90

Software Package:

Software Name	Purpose
XENGEN	data collection
XENGEN	data reduction
X-PLOR	model building
X-PLOR	refinement
XENGEN	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1997-02-18 
• Released Date: 1998-02-25 
Deposition Author(s): Cole, L.B., Chu, N., Kilpatrick, J.M., Volanakis, J.E., Narayana, S.V.L., Babu, Y.S.

Revision History 

• Version 1.0: 1998-02-25
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance