1JBU

Coagulation Factor VII Zymogen (EGF2/Protease) in Complex with Inhibitory Exosite Peptide A-183


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

The factor VII zymogen structure reveals reregistration of beta strands during activation.

Eigenbrot, C.Kirchhofer, D.Dennis, M.S.Santell, L.Lazarus, R.A.Stamos, J.Ultsch, M.H.

(2001) Structure 9: 627-636

  • DOI: 10.1016/s0969-2126(01)00624-4
  • Primary Citation of Related Structures:  
    1JBU

  • PubMed Abstract: 
  • Coagulation factor VIIa (FVIIa) contains a Trypsin-like serine protease domain and initiates the cascade of proteolytic events leading to Thrombin activation and blood clot formation. Vascular injury allows formation of the complex between circulating FVIIa and its cell surface bound obligate cofactor, Tissue Factor (TF) ...

    Coagulation factor VIIa (FVIIa) contains a Trypsin-like serine protease domain and initiates the cascade of proteolytic events leading to Thrombin activation and blood clot formation. Vascular injury allows formation of the complex between circulating FVIIa and its cell surface bound obligate cofactor, Tissue Factor (TF). Circulating FVIIa is nominally activated but retains zymogen-like character and requires TF in order to complete the zymogen-to-enzyme transition. The manner in which TF exerts this effect is unclear. The structure of TF/FVIIa is known. Knowledge of the zymogen structure is helpful for understanding the activation transition in this system.


    Related Citations: 
    • A Novel Exosite on Coagulation Factor VIIa and its Molecular Interactions with a New Class of Peptide Inhibitors
      Roberge, M., Santell, L., Dennis, M.S., Eigenbrot, C., Dwyer, M.A., Lazarus, R.A.
      () To be published --: --
    • The Crystal Structure of the Complex of Blood Coagulation Factor VIIa with Soluble Tissue Factor
      Banner, D.W., D'Arcy, A., Chene, C., Winkler, F.K., Guha, A., Konigsberg, W.H., Nemerson, Y., Kirchhofer, D.
      (1996) Nature 380: 41
    • Structure of Extracellular Tissue Factor Complexed with Factor VIIa Inhibited with a BPTI Mutant
      Zhang, E., St.Charles, R., Tulinsky, A.
      (1999) J Mol Biol 285: 2089
    • Crystal Structure of Active Site-inhibited Human Coagulation Factor VIIa (des-Gla)
      Kemball-Cook, G., Johnson, D.J., Tuddenham, E.G., Harlos, K.
      (1999) J Struct Biol 127: 213
    • Structure of Human Factor VIIa and its Implications for the Triggering of Blood Coagulation
      Pike, A.C., Brzozowski, A.M., Roberts, S.M., Olsen, O.H., Persson, E.
      (1999) Proc Natl Acad Sci U S A 96: 8925
    • Peptide Exosite Inhibitors of Factor VIIa as Anticoagulants
      Dennis, M.S., Eigenbrot, C., Skelton, N.J., Ultsch, M.H., Santell, L., Dwyer, M.A., O'Connell, M.P., Lazarus, R.A.
      (2000) Nature 404: 465

    Organizational Affiliation

    Department of Protein Engineering and, Genentech, Inc., South, San Francisco, CA, USA. eigenbrot.c@gene.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
COAGULATION FACTOR VIIA [auth H]254Homo sapiensMutation(s): 0 
Gene Names: F7
EC: 3.4.21.21
UniProt & NIH Common Fund Data Resources
Find proteins for P08709 (Homo sapiens)
Explore P08709 
Go to UniProtKB:  P08709
PHAROS:  P08709
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
COAGULATION FACTOR VIIB [auth L]63Homo sapiensMutation(s): 0 
Gene Names: F7
EC: 3.4.21.21
UniProt & NIH Common Fund Data Resources
Find proteins for P08709 (Homo sapiens)
Explore P08709 
Go to UniProtKB:  P08709
PHAROS:  P08709
Protein Feature View
Expand
  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Peptide exosite inhibitor A-183C [auth X]15Escherichia coliMutation(s): 0 
Gene Names: synthetic construct
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BEN
Query on BEN

Download Ideal Coordinates CCD File 
E [auth H]BENZAMIDINE
C7 H8 N2
PXXJHWLDUBFPOL-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth H]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.44α = 90
b = 84.51β = 90
c = 84.84γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
SCALEPACKdata scaling
AMoREphasing
X-PLORrefinement

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-07-11
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2018-01-24
    Changes: Advisory, Database references
  • Version 1.4: 2018-01-31
    Changes: Database references