5YUP

Crystal Structure of the Fab fragment of FVIIa antibody mAb4F5

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Crystal structure, epitope, and functional impact of an antibody against a superactive FVIIa provide insights into allosteric mechanism.

Jiang, L.G., Xie, X., Li, J., Persson, E., Huang, M.D.

(2019) Res Pract Thromb Haemost 3: 412-419

  • DOI: https://doi.org/10.1002/rth2.12211
  • Primary Citation of Related Structures:  
    5YUP

  • PubMed Abstract: 

    Blood coagulation factor VIIa (FVIIa) plays its critical physiological role in the initiation of hemostasis. Even so, recombinant FVIIa is successfully used as a bypassing agent for factor VIII or IX in the treatment of bleeds in patients with severe hemophilia with inhibitors. To investigate the utility of more potent FVIIa variants with enhanced intrinsic activity, molecules such as V21D/E154V/M156Q-FVIIa (FVIIa DVQ ) were designed.

    • Organizational Affiliation: 

    College of Chemistry National & Local Joint Biomedical Engineering Research Center on Photodynamic Technologies Fuzhou University Fuzhou China.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
the heavy chain of the Fab fragment of FVIIa antibody mAb4F5A [auth H]219Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
the light chain of the Fab fragment of FVIIa antibody mAb4F5B [auth L]215Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.64α = 90
b = 141.64β = 90
c = 141.64γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31400637

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-19
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description