2FIB

RECOMBINANT HUMAN GAMMA-FIBRINOGEN CARBOXYL TERMINAL FRAGMENT (RESIDUES 143-411) COMPLEXED TO THE PEPTIDE GLY-PRO-ARG-PRO AT PH 6.0


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The primary fibrin polymerization pocket: three-dimensional structure of a 30-kDa C-terminal gamma chain fragment complexed with the peptide Gly-Pro-Arg-Pro.

Pratt, K.P.Cote, H.C.Chung, D.W.Stenkamp, R.E.Davie, E.W.

(1997) Proc.Natl.Acad.Sci.USA 94: 7176-7181

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • After vascular injury, a cascade of serine protease activations leads to the conversion of the soluble fibrinogen molecule into fibrin. The fibrin monomers then polymerize spontaneously and noncovalently to form a fibrin gel. The primary interaction ...

    After vascular injury, a cascade of serine protease activations leads to the conversion of the soluble fibrinogen molecule into fibrin. The fibrin monomers then polymerize spontaneously and noncovalently to form a fibrin gel. The primary interaction of this polymerization reaction is between the newly exposed N-terminal Gly-Pro-Arg sequence of the alpha chain of one fibrin molecule and the C-terminal region of a gamma chain of an adjacent fibrin(ogen) molecule. In this report, the polymerization pocket has been identified by determining the crystal structure of a 30-kDa C-terminal fragment of the fibrin(ogen) gamma chain complexed with the peptide Gly-Pro-Arg-Pro. This peptide mimics the N terminus of the alpha chain of fibrin. The conformational change in the protein upon binding the peptide is subtle, with electrostatic interactions primarily mediating the association. This is consistent with biophysical experiments carried out over the last 50 years on this fundamental polymerization reaction.


    Organizational Affiliation

    Department of Biochemistry, University of Washington, Seattle, WA 98195, USA. kpratt@u.washington.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FIBRINOGEN
A
269Homo sapiensMutation(s): 0 
Gene Names: FGG
Find proteins for P02679 (Homo sapiens)
Go to Gene View: FGG
Go to UniProtKB:  P02679
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
GLY-PRO-ARG-PRO
B
4N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.186 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 37.330α = 90.00
b = 68.200β = 105.02
c = 47.600γ = 90.00
Software Package:
Software NamePurpose
XTALVIEWrefinement
X-PLORmodel building
RIGAKUdata collection
X-PLORrefinement
RIGAKUdata reduction
RIGAKUdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-10-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance