1JBU

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.204 

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


  • 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 circulatin ...

    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: 
    • 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
    • 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.USA 96: 8925
    • 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
    • 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 --: --


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
COAGULATION FACTOR VII
H
254Homo sapiensGene Names: F7
EC: 3.4.21.21
Find proteins for P08709 (Homo sapiens)
Go to Gene View: F7
Go to UniProtKB:  P08709
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
COAGULATION FACTOR VII
L
63Homo sapiensGene Names: F7
EC: 3.4.21.21
Find proteins for P08709 (Homo sapiens)
Go to Gene View: F7
Go to UniProtKB:  P08709
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Peptide exosite inhibitor A-183
X
15N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
H
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
BEN
Query on BEN

Download SDF File 
Download CCD File 
H
BENZAMIDINE
C7 H8 N2
PXXJHWLDUBFPOL-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 67.440α = 90.00
b = 84.510β = 90.00
c = 84.840γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
SCALEPACKdata scaling
AMoREphasing
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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