Biological Assembly 1  

 3D View: Structure | Electron Density

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 67.40 kDa 
• Atom Count: 5022 
• Residue Count: 570 
• Unique protein chains: 1

1DLE

FACTOR B SERINE PROTEASE DOMAIN

• DOI: 10.2210/pdb1DLE/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 1999-12-09 Released: 2000-12-13 
• Deposition Author(s): Jing, H., Xu, Y., Carson, M., Moore, D., Macon, K.J., Volanakis, J.E., Narayana, S.V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.249 
• R-Value Work: 0.209 
• R-Value Observed: 0.210 

Literature

New structural motifs on the chymotrypsin fold and their potential roles in complement factor B.

Jing, H., Xu, Y., Carson, M., Moore, D., Macon, K.J., Volanakis, J.E., Narayana, S.V.

(2000) EMBO J 19: 164-173

• PubMed: 10637221 
• DOI: 10.1093/emboj/19.2.164
• Primary Citation of Related Structures:  
  1DLE


• PubMed Abstract: 
  

Factor B and C2 are two central enzymes for complement activation. They are multidomain serine proteases and require cofactor binding for full expression of proteolytic activities. We present a 2.1 A crystal structure of the serine protease domain of factor B. It shows a number of structural motifs novel to the chymotrypsin fold, which by sequence homology are probably present in C2 as well. These motifs distribute characteristically on the protein surface. Six loops surround the active site, four of which shape substrate-binding pockets. Three loops next to the oxyanion hole, which typically mediate zymogen activation, are much shorter or absent. Three insertions including the linker to the preceding domain bulge from the side opposite to the active site. The catalytic triad and non-specific substrate-binding site display active conformations, but the oxyanion hole displays a zymogen-like conformation. The bottom of the S1 pocket has a negative charge at residue 226 instead of the typical 189 position. These unique structural features may play different roles in domain-domain interaction, cofactor binding and substrate binding.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEMENT FACTOR B	A, B	298	Homo sapiens	Mutation(s): 0  Gene Names: CFB, BF, BFD EC: 3.4.21.47
Find proteins for P00751 (Homo sapiens) Explore P00751  Go to UniProtKB:  P00751
NIH Common Fund Data Resources
PHAROS  P00751 GTEx  ENSG00000243649

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.249 
• R-Value Work: 0.209 
• R-Value Observed: 0.210 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.643	α = 90
b = 74.259	β = 95.55
c = 73.258	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
SCALEPACK	data scaling
AMoRE	phasing
XTALVIEW	refinement
MLPHARE	phasing
DMMulti	model building
DENZO	data reduction
DMMulti	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-12-09 
• Released Date: 2000-12-13 
Deposition Author(s): Jing, H., Xu, Y., Carson, M., Moore, D., Macon, K.J., Volanakis, J.E., Narayana, S.V.

Revision History 

• Version 1.0: 2000-12-13
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2019-07-24
  Changes: Data collection, Refinement description
• Version 1.5: 2019-11-13
  Changes: Database references, Structure summary