6B77

Structures of the two-chain human plasma factor XIIa co-crystallized with potent inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report



Literature

Structures of human plasma beta-factor XIIa cocrystallized with potent inhibitors.

Dementiev, A.Silva, A.Yee, C.Li, Z.Flavin, M.T.Sham, H.Partridge, J.R.

(2018) Blood Adv 2: 549-558

  • DOI: 10.1182/bloodadvances.2018016337
  • Primary Citation of Related Structures:  
    6B74, 6B77

  • PubMed Abstract: 
  • Activated factor XIIa (FXIIa) is a serine protease that has received a great deal of interest in recent years as a potential target for the development of new antithrombotics. Despite the strong interest in obtaining structural information, only the ...

    Activated factor XIIa (FXIIa) is a serine protease that has received a great deal of interest in recent years as a potential target for the development of new antithrombotics. Despite the strong interest in obtaining structural information, only the structure of the FXIIa catalytic domain in its zymogen conformation is available. In this work, reproducible experimental conditions found for the crystallization of human plasma β-FXIIa and crystal growth optimization have led to determination of the first structure of the active form of the enzyme. Two crystal structures of human plasma β-FXIIa complexed with small molecule inhibitors are presented herein. The first is the noncovalent inhibitor benzamidine. The second is an aminoisoquinoline containing a boronic acid-reactive group that targets the catalytic serine. Both benzamidine and the aminoisoquinoline bind in a canonical fashion typical of synthetic serine protease inhibitors, and the protease domain adopts a typical chymotrypsin-like serine protease active conformation. This novel structural data explains the basis of the FXII activation, provides insights into the enzymatic properties of β-FXIIa, and is a great aid toward the further design of protease inhibitors for human FXIIa.


    Organizational Affiliation

    Global Blood Therapeutics, Inc, South San Francisco, CA.



Macromolecules
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Coagulation factor XIIA9Homo sapiensMutation(s): 0 
Gene Names: F12
EC: 3.4.21.38
Find proteins for P00748 (Homo sapiens)
Explore P00748 
Go to UniProtKB:  P00748
NIH Common Fund Data Resources
PHAROS  P00748
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Coagulation factor XIIB243Homo sapiensMutation(s): 0 
Gene Names: F12
EC: 3.4.21.38
Find proteins for P00748 (Homo sapiens)
Explore P00748 
Go to UniProtKB:  P00748
NIH Common Fund Data Resources
PHAROS  P00748
Protein Feature View
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 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
2 N-Glycosylation
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CWV
Query on CWV

Download CCD File 
B
[3-(1-aminoisoquinolin-6-yl)phenyl]boronic acid
C15 H13 B N2 O2
CCUGLTODPQTEBR-UHFFFAOYSA-N
 Ligand Interaction
IOD
Query on IOD

Download CCD File 
B
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
SO4
Query on SO4

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

Download CCD File 
B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.174 
  • Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.402α = 90
b = 79.402β = 90
c = 122.246γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-03-21
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary